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GitLab

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<h3>

Fabian Klötzl pushed to branch master

at <a href="https://salsa.debian.org/med-team/andi">Debian Med / andi</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/andi/commit/e28213ab68584bb8e6d4a857d8d1c4afd958de3e">e28213ab</a></strong>

<div>

<span>by Fabian Klötzl</span>

<i>at 2018-02-26T15:00:32+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Imported Upstream version 0.12</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/andi/commit/09638a2eab8b14c70a13c4ad8bbbc5d3340a52d7">09638a2e</a></strong>

<div>

<span>by Fabian Klötzl</span>

<i>at 2018-02-26T15:00:33+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/0.12'

Upstream version 0.12

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/andi/commit/1012cec549f8d12d7510385019949b78c3829938">1012cec5</a></strong>

<div>

<span>by Fabian Klötzl</span>

<i>at 2018-02-26T15:15:26+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">prepare for debian/0.12-1

</pre>

</li>

</ul>

<h4>22 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">

.gitignore

</a>

</li>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

.travis.yml

</a>

</li>

<li class="file-stats">

<a href="#d5b4de16d947214ec306bd57bed1bd23a939b5f9">

Makefile.am

</a>

</li>

<li class="file-stats">

<a href="#5b785a47c2276fad59c8479f07f96b491e3db561">

andi-manual.pdf

</a>

</li>

<li class="file-stats">

<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">

configure.ac

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#c4c79141c51db1c8b5e8ca9f23d64d8a9142d6da">

docs/andi.1.in

</a>

</li>

<li class="file-stats">

<a href="#866c333caed2725512f59600c796c8e0be2b69ff">

docs/manual/andi-manual.tex

</a>

</li>

<li class="file-stats">

<a href="#28db630a02e8ffab6561cceefc6c8e0426b5e1b0">

scripts/_andi

</a>

</li>

<li class="file-stats">

<a href="#e4121eb35479a00bb2becf6c512563545bb34482">

src/andi.c

</a>

</li>

<li class="file-stats">

<a href="#e611a4867dd9a0b53115c8847a0302431c5da23d">

src/dist_hack.h

</a>

</li>

<li class="file-stats">

<a href="#010ebeab960fdcf8c02bab9f78bc704a379c3490">

src/esa.c

</a>

</li>

<li class="file-stats">

<a href="#c30c220576b993ebc2341d565eb0ff0c4a10da82">

src/global.h

</a>

</li>

<li class="file-stats">

<a href="#0f3044ba93433ecc1c927c85984cb8dc55b76b9f">

src/io.c

</a>

</li>

<li class="file-stats">

<a href="#93f5f7039d98b42c276a3759cba8ff5bea5a2d7e">

src/model.c

</a>

</li>

<li class="file-stats">

<a href="#6647cd41afbb7c523f68ba302195e484f7ac5b4a">

src/process.c

</a>

</li>

<li class="file-stats">

<a href="#01a89d148d2434a88bba979e1ef4be45506178a5">

test/Makefile.am

</a>

</li>

<li class="file-stats">

<a href="#819e7d39af1d85fdb7ad927da43590676d2e5a2e">

<span class="new-file">

+

test/low_homo.sh

</span>

</a>

</li>

<li class="file-stats">

<a href="#a6c3dd442629f79bf8c5fd2561ef574096e0b943">

<span class="new-file">

+

test/nan.sh

</span>

</a>

</li>

<li class="file-stats">

<a href="#4c66163cb3f8754139de01c9a49d0f51241d0226">

test/test_join.sh

</a>

</li>

<li class="file-stats">

<a href="#047ffddd3115a4a27235eda8eb9e856096824659">

<span class="new-file">

+

test/test_process.c

</span>

</a>

</li>

<li class="file-stats">

<a href="#c1ae1894c1ffe40463c0bf3450a17d5e639a24f3">

test/test_random.sh

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="a5cc2925ca8258af241be7e5b0381edf30266302">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>

<hr>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,6 +58,7 @@ test-driver</td>

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<td class="diff-line-num old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

58

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<td class="diff-line-num new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

58

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">test_esa</span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

59

</td>

<td class="diff-line-num new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

59

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">test_seq</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

60

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<td class="diff-line-num new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

60

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">test_fasta</span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

61

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">test_process</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

61

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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

62

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">*.trs</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

62

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<td class="diff-line-num new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<td class="diff-line-num new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

64

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"># Coverage</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="na" style="color: teal;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">cpp</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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<td class="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="na" style="color: teal;">os</span><span class="pi">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">linux</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<td class="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;"># - osx</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="na" style="color: teal;">compiler</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">gcc</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">clang</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,9 +10,9 @@ addons:</td>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml">      <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml">    <span class="na" style="color: teal;">packages</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml">      <span class="pi">-</span> <span class="s" style="color: #d14;">cmake</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml">      <span class="pi">-</span> <span class="s" style="color: #d14;">g++-4.8</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml">      <span class="pi">-</span> <span class="s" style="color: #d14;">libglib2.0-dev</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml">      <span class="pi">-</span> <span class="s" style="color: #d14;">libgsl0-dev</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"><span class="na" style="color: teal;">install</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">export LIBDIVDIR="$HOME/libdivsufsort"</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">pip install --user cpp-coveralls</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,30 +21,26 @@ install:</td>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cd libdivsufsort-master && mkdir build && cd build</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_INSTALL_PREFIX="$LIBDIVDIR" ..</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">make && make install</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "${TRAVIS_OS_NAME}" = "osx" ]; then brew install gsl; fi</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "${TRAVIS_OS_NAME}" = "osx" ]; then brew install glib; fi</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"><span class="na" style="color: teal;">before_install</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$CXX" = "g++" ]; then export CXX="g++-4.8" CC="gcc-4.8"; fi</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC32" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 90</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

33

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml"><span class="na" style="color: teal;">script</span><span class="pi">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

34

</td>

<td class="diff-line-num new_line old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC34" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;"><span class="idiff left right">export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$LIBDIVDIR/lib</span>"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;"><span class="idiff left right">CONFIGURE_FLAGS="</span>"</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

35

</td>

<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">export LD_LIBRARY_PATH="$LIBDIVDIR:$LIBDIVDIR/lib"</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

28

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">export LIBRARY_PATH="$LIBDIVDIR:$LIBRARY_PATH"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC29" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">cd $TRAVIS_BUILD_DIR</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

30

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC30" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">autoreconf -fvi -Im4</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">export MYFLAGS="-fprofile-arcs -ftest-coverage -I$LIBDIVDIR/include"</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

40

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<td class="diff-line-num new_line old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC40" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">./configure --enable-unit-tests LDFLAGS="-L$LIBDIVDIR/lib" CFLAGS="$MYFLAGS" CXXFLAGS="$MYFLAGS"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">if [ "${CC}" = "clang" ]; then export CONFIGURE_FLAGS="--disable-openmp"; fi</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">./configure $CONFIGURE_FLAGS --enable-unit-tests LDFLAGS="-L$LIBDIVDIR/lib" CFLAGS="$MYFLAGS" CXXFLAGS="$MYFLAGS"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC34" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

42

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<td class="diff-line-num new_line old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC42" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">make check</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

35

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">make check<span class="idiff left right"> || cat ./test-suite.log || exit 1</span></span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">export MYFLAGS="-I$LIBDIVDIR/include"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

44

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<td class="diff-line-num new_line old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC44" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">./configure --enable-unit-tests LDFLAGS="-L$LIBDIVDIR/lib" CFLAGS="$MYFLAGS" CXXFLAGS="$MYFLAGS"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

45

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<td class="diff-line-num new_line old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC45" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">make distcheck DISTCHECK_CONFIGURE_FLAGS="LDFLAGS=\"-L$LIBDIVDIR/lib\" CFLAGS=\"-I$LIBDIVDIR/include\" CXXFLAGS=\"-I$LIBDIVDIR/include\""</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

37

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">./configure <span class="idiff left right">$CONFIGURE_FLAGS </span>--enable-unit-tests LDFLAGS="-L$LIBDIVDIR/lib" CFLAGS="$MYFLAGS" CXXFLAGS="$MYFLAGS"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">make distcheck DISTCHECK_CONFIGURE_FLAGS="LDFLAGS=\"-L$LIBDIVDIR/lib\" CFLAGS=\"-I$LIBDIVDIR/include\" CXXFLAGS=\"-I$LIBDIVDIR/include\"<span class="idiff left right"> $CONFIGURE_FLAGS</span>"</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">tar xzvf andi-*.tar.gz</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

47

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">cd andi-*</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

48

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<td class="diff-line-num new_line old" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">./configure --enable-unit-tests --without-libdivsufsort</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">./configure <span class="idiff left right">$CONFIGURE_FLAGS </span>--enable-unit-tests --without-libdivsufsort</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC42" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

50

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<td class="diff-line-num new_line old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">make check</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">make check<span class="idiff left right"> || cat ./test-suite.log || exit 1</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">cd ..</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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45

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="yaml"><span class="na" style="color: teal;">after_success</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$<span class="idiff left right">{TRAVIS_OS_NAME}" = "linux" -a "$CXX" = "g++-4.8</span>" ]; then coveralls --exclude libdivsufsort-master -E '^andi-.*' --exclude libs --exclude test --gcov `which gcov-4.8` --gcov-options '\-lp'; fi</span></span></pre>

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<td class="diff-line-num new old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$<span class="idiff left right">CXX" = "g++</span>" ]; then coveralls --exclude libdivsufsort-master -E '^andi-.*' --exclude libs --exclude test --gcov `which gcov-4.8` --gcov-options '\-lp'; fi</span></span></pre>

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<br>

</li>

<li id="d5b4de16d947214ec306bd57bed1bd23a939b5f9">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#d5b4de16d947214ec306bd57bed1bd23a939b5f9"><strong>Makefile.am</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,8 @@ SUBDIRS+= test</td>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"><span class="nv" style="color: teal;">AM_TESTS_ENVIRONMENT</span><span class="o" style="font-weight: 600;">=</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make">  <span class="nv" style="color: teal;">RANDOM_SEED</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'@SEED@'</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>RANDOM_SEED <span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="make"><span class="nv" style="color: teal;">TESTS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">test</span>/test_esa <span class="nb" style="color: #0086b3;">test</span>/test_seq <span class="nb" style="color: #0086b3;">test</span>/test_extra.sh <span class="nb" style="color: #0086b3;">test</span>/test_random.sh <span class="nb" style="color: #0086b3;">test</span>/test_join.sh</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"><span class="nv" style="color: teal;">XFAIL_TESTS</span><span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"><span class="nv" style="color: teal;">TESTS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(XFAIL_TESTS)</span> <span class="nb" style="color: #0086b3;">test</span>/nan.sh <span class="nb" style="color: #0086b3;">test</span>/low_homo.sh <span class="nb" style="color: #0086b3;">test</span>/test_esa <span class="nb" style="color: #0086b3;">test</span>/test_seq <span class="nb" style="color: #0086b3;">test</span>/test_extra.sh <span class="nb" style="color: #0086b3;">test</span>/test_random.sh <span class="nb" style="color: #0086b3;">test</span>/test_join.sh <span class="nb" style="color: #0086b3;">test</span>/test_process</span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"><span class="nl">$(TESTS)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">src/andi</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"></span>

</pre>

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<br>

</li>

<li id="5b785a47c2276fad59c8479f07f96b491e3db561">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#5b785a47c2276fad59c8479f07f96b491e3db561"><strong>andi-manual.pdf</strong></a>

<hr>

No preview for this file type

<br>

</li>

<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>

<hr>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">AC_INIT([andi], [0.1<span class="idiff left right">1</span>])</span>

</pre>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">AM_INIT_AUTOMAKE([-Wall foreign<span class="idiff left right"> </span>])</span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">AC_INIT([andi], [0.1<span class="idiff left right">2</span>])</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">AM_INIT_AUTOMAKE([-Wall foreign])</span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AC_CONFIG_MACRO_DIR([m4])</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -78,8 +78,7 @@ AC_ARG_WITH([seed],</td>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">AC_SUBST([SEED])</span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">if test "x${try_unit_tests}" = xyes; then</span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">AS_IF([test "x${try_unit_tests}" = xyes], [</span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext">     have_glib=yes</span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext">     PKG_CHECK_MODULES([GLIB], [glib-2.0], [], [have_glib=no])</span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,7 +87,7 @@ if test "x${try_unit_tests}" = xyes; then</td>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext">     fi</span>

</pre>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext">     AX_CXX_COMPILE_STDCXX_11([],[mandatory])</span>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext"><span class="idiff left right">fi</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"><span class="idiff left right">])</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"></span>

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<td class="diff-line-num old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"># Check for various headers including those used by libdivsufsort.</span>

</pre>

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</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">andi (0.1<span class="idiff left right">1-2</span>) UNRELEASED; urgency=medium</span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">andi (0.1<span class="idiff left right">2-1</span>) UNRELEASED; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">  * Team upload.</span>

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">  [ Fabian Klötzl ]</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">  * Remove useless dh-autoreconf build dependency</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  * Import new upstream release</span>

</pre>

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7

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  [ Steffen Moeller ]</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">  * debian/upstream/metadata: added refs to registries</span>

</pre>

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<br>

</li>

<li id="c4c79141c51db1c8b5e8ca9f23d64d8a9142d6da">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#c4c79141c51db1c8b5e8ca9f23d64d8a9142d6da"><strong>docs/andi.1.in</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH ANDI "1" "2017-0<span class="idiff left right">6-30</span>" "@VERSION@" "andi manual"</span>

</pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH ANDI "1" "2017-0<span class="idiff left right">9-17</span>" "@VERSION@" "andi manual"</span>

</pre>

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">.SH NAME</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">andi \- estimates evolutionary distance</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.B andi</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">[\fI<span class="idiff left right">-jlv\fR] [\fI-b INT\fR] [\fI-p FLOAT\fR] [\fI-m MODEL\fR] [\fI-t INT</span>\fR] \fIFILES\fR...</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">[\fI<span class="idiff left right">OPTIONS...</span>\fR] \fIFILES\fR...</span>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">.SH DESCRIPTION</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">.TP</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">\fBandi\fR estimates the evolutionary distance between closely related genomes. For this \fBandi\fR reads the input sequences from \fIFASTA\fR files and computes the pairwise anchor distance. The idea behind this is explained in a paper by Haubold et al. (2015).</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,10 +11,10 @@ andi \- estimates evolutionary distance</td>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">The output is a symmetrical distance matrix in \fIPHYLIP\fR format, with each entry representing divergence with a positive real number. A distance of zero means that two sequences are identical, whereas other values are estimates for the nucleotide substitution rate (Jukes-Cantor corrected). For technical reasons the comparison might fail and no estimate can be computed. In such cases \fInan\fR is printed. This either means that the input sequences were too short (<200bp) or too diverse (K>0.5) for our method to work properly.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">.SH OPTIONS</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">.TP</span>

</pre>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">\fB\-b\fR<span class="idiff left right">, \fB\-\-bootstrap\fR <INT></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-b\fR<span class="idiff left right"> \fIINT\fR, \fB\-\-bootstrap\fR=\fIINT\fR</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Compute multiple distance matrices, with \fIn-1\fR bootstrapped from the first. See the paper Klötzl & Haubold (2016) for a detailed explanation.</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">.TP</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">\fB--file-of-filenames\fR<span class="idiff left right"> <FILE></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB--file-of-filenames\fR<span class="idiff left right">=\fIFILE\fR</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Usually, \fBandi\fR is called with the filenames as commandline arguments. With this option the filenames may also be read from a file itself, with one name per line. Use a single dash (\fB'-'\fR) to read from stdin.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">.TP</span>

</pre>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">\fB\-j\fR, \fB\-\-join\fR</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,13 +23,16 @@ Use this mode if each of your \fIFASTA\fR files represents one assembly with num</td>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">\fB\-l\fR, \fB\-\-low-memory\fR</span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">In multithreaded mode, \fBandi\fR requires memory linear to the amount of threads. The low memory mode changes this to a constant demand independent from the used number of threads. Unfortunately, this comes at a significant runtime cost.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">.TP</span>

</pre>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">\fB\-m\fR<span class="idiff left right">, \fB\-\-model\fR <Raw|JC|Kimura></span></span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"><span class="idiff left right">Different models of nucleotide evolution are supported</span>. By default the Jukes-Cantor correction is used.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-m\fR<span class="idiff left right"> \fIMODEL\fR, \fB\-\-model\fR=\fIMODEL\fr</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"><span class="idiff left right">Set the nucleotide evolution model to one of 'Raw', 'JC', or 'Kimura'</span>. By default the Jukes-Cantor correction is used.</span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">.TP</span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">\fB\-p\fR <span class="idiff left right"><FLOAT></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-p\fR <span class="idiff left right">\fIFLOAT\fR</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Significance of an anchor; default: 0.025.</span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">.TP</span>

</pre>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">\fB\-t\fR, \fB\-\-threads\fR <INT></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB--progress\fR[=\fIWHEN\fR]</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Print a progress bar. \fIWHEN\fR can be 'auto' (default if omitted), 'always', or 'never'.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.TP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-t\fR \fIINT\fR, \fB\-\-threads\fR=\fIINT\fR</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

33

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">The number of threads to be used; by default, all available processors are used.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">.br</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

35

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Multithreading is only available if \fBandi\fR was compiled with OpenMP support.</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,7 +41,7 @@ Multithreading is only available if \fBandi\fR was compiled with OpenMP support.</td>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">By default \fBandi\fR outputs the full names of sequences, optionally padded with spaces, if they are shorter than ten characters. Names longer than ten characters may lead to problems with downstream tools. With this switch names will be truncated.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">.TP</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">\fB\-v\fR, \fB\-\-verbose\fR</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

41

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<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">Prints additional information. Apply multiple times for extra verboseness.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

44

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Prints additional information<span class="idiff left right">, including the amount of found homology</span>. Apply multiple times for extra verboseness.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">.TP</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Prints the synopsis and an explanation of available options.</span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,7 +49,7 @@ Prints the synopsis and an explanation of available options.</td>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">\fB\-\-version\fR</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

47

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">Outputs version information and acknowledgments.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">.SH COPYRIGHT</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">Copyright \(co 2014 - 201<span class="idiff left right">6</span> Fabian Klötzl</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">Copyright \(co 2014 - 201<span class="idiff left right">7</span> Fabian Klötzl</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">License GPLv3+: GNU GPL version 3 or later.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">.br</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">This is free software: you are free to change and redistribute it.</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="866c333caed2725512f59600c796c8e0be2b69ff">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#866c333caed2725512f59600c796c8e0be2b69ff"><strong>docs/manual/andi-manual.tex</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -106,61 +106,62 @@ This document is release under the Creative Commons Attribution Share-Alike lice</td>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="tex">The easiest way to install <span class="k" style="font-weight: 600;">\andi</span> is via a package manager. This also handles all dependencies for you.</span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="tex"></span>

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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="tex"><span class="k" style="font-weight: 600;">\noindent</span> Debian and Ubuntu<span class="idiff left right"> (since 16.04)</span>:</span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="tex"><span class="k" style="font-weight: 600;">\noindent</span> Debian and Ubuntu:</span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="tex"><span class="nt" style="color: navy;">\begin{lstlisting}</span></span>

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<td class="diff-line-num old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="tex">~ <span class="c" style="color: #998; font-style: italic;">%  sudo apt-get install andi</span></span>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="tex"><span class="nt" style="color: navy;">\end{lstlisting}</span></span>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="tex"></span>

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<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="tex"><span class="k" style="font-weight: 600;">\noindent</span> <span class="idiff left right">OS X</span> with homebrew:</span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="tex"><span class="k" style="font-weight: 600;">\noindent</span> <span class="idiff left right">macOS</span> with homebrew:</span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="tex"><span class="nt" style="color: navy;">\begin{lstlisting}</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="tex">~ <span class="c" style="color: #998; font-style: italic;">%  brew install homebrew/science/andi</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="tex"><span class="nt" style="color: navy;">\end{lstlisting}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="tex"><span class="k" style="font-weight: 600;">\noindent</span> ArchLinux:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="tex"><span class="k" style="font-weight: 600;">\noindent</span> ArchLinux<span class="idiff left right"> AUR package with aura</span>:</span>

</pre>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="tex"><span class="nt" style="color: navy;">\begin{lstlisting}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="tex">~ <span class="c" style="color: #998; font-style: italic;">%  aura -A andi</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="tex"><span class="nt" style="color: navy;">\end{lstlisting}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="tex"><span class="k" style="font-weight: 600;">\andi</span> is intended to run in a <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>Unix<span class="p">}</span> commandline such as <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="nb" style="color: #0086b3;">bash</span><span class="p">$</span> or <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="nb" style="color: #0086b3;">zsh</span><span class="p">$</span>. All examples in this document are also intended for that environment. You can verify that <span class="k" style="font-weight: 600;">\andi</span> was installed correctly by executing <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="nb" style="color: #0086b3;">andi </span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">h</span><span class="p">$</span>. This should give you a list of all available options (see Section~<span class="k" style="font-weight: 600;">\ref</span><span class="p">{</span>sec:options<span class="p">}</span>).</span>

</pre>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="tex"><span class="k" style="font-weight: 600;">\andi</span> is intended to <span class="idiff left right">be </span>run in a <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>Unix<span class="p">}</span> commandline such as <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="nb" style="color: #0086b3;">bash</span><span class="p">$</span> or <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="nb" style="color: #0086b3;">zsh</span><span class="p">$</span>. All examples in this document are also intended for that environment. You can verify that <span class="k" style="font-weight: 600;">\andi</span> was installed correctly by executing <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="nb" style="color: #0086b3;">andi </span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">h</span><span class="p">$</span>. This should give you a list of all available options (see Section~<span class="k" style="font-weight: 600;">\ref</span><span class="p">{</span>sec:options<span class="p">}</span>).</span>

</pre>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="tex"><span class="k" style="font-weight: 600;">\section</span><span class="p">{</span>Source Package<span class="p">}</span> <span class="k" style="font-weight: 600;">\label</span><span class="p">{</span>sub:regular<span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="tex"><span class="idiff left right">D</span>ownload the latest <span class="k" style="font-weight: 600;">\href</span><span class="p">{</span>https://github.com/EvolBioInf/andi/releases<span class="p">}{</span>release<span class="p">}</span> from GitHub. Please note, that <span class="k" style="font-weight: 600;">\andi</span> requires the <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>Gnu Scientific Library<span class="p">}</span> and optionally <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>libdivsufsort<span class="p">}</span><span class="k" style="font-weight: 600;">\footnote</span><span class="p">{</span><span class="k" style="font-weight: 600;">\url</span><span class="p">{</span>https://github.com/y-256/libdivsufsort<span class="p">}}</span> for optimal performance <span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>divsufsort<span class="p">}</span>. If you wish to install <span class="k" style="font-weight: 600;">\andi</span> without <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>libdivsufsort<span class="p">}</span>, consult Section~<span class="k" style="font-weight: 600;">\ref</span><span class="p">{</span>sub:wo-divsufsort<span class="p">}</span>.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="tex"><span class="idiff left">To build </span><span class="k" style="font-weight: 600;"><span class="idiff">\andi</span></span><span class="idiff right"> from source, d</span>ownload the latest <span class="k" style="font-weight: 600;">\href</span><span class="p">{</span>https://github.com/EvolBioInf/andi/releases<span class="p">}{</span>release<span class="p">}</span> from GitHub. Please note, that <span class="k" style="font-weight: 600;">\andi</span> requires the <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>Gnu Scientific Library<span class="p">}</span> and optionally <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>libdivsufsort<span class="p">}</span><span class="k" style="font-weight: 600;">\footnote</span><span class="p">{</span><span class="k" style="font-weight: 600;">\url</span><span class="p">{</span>https://github.com/y-256/libdivsufsort<span class="p">}}</span> for optimal performance <span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>divsufsort<span class="p">}</span>. If you wish to install <span class="k" style="font-weight: 600;">\andi</span> without <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>libdivsufsort<span class="p">}</span>, consult Section~<span class="k" style="font-weight: 600;">\ref</span><span class="p">{</span>sub:wo-divsufsort<span class="p">}</span>.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="tex">Once you have downloaded the package, unzip it and change into the newly created directory. </span>

</pre>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="tex"><span class="nt" style="color: navy;">\begin{lstlisting}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="tex">~ <span class="c" style="color: #998; font-style: italic;">%  tar -xzvf andi-0.1<span class="idiff left right">1</span>.tar.gz</span></span>

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="tex">~ <span class="c" style="color: #998; font-style: italic;">%  cd andi-0.1<span class="idiff left right">1</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="tex">~ <span class="c" style="color: #998; font-style: italic;">%  tar -xzvf andi-0.1<span class="idiff left right">2</span>.tar.gz</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="tex">~ <span class="c" style="color: #998; font-style: italic;">%  cd andi-0.1<span class="idiff left right">2</span></span></span>

</pre>

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138

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138

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="tex"><span class="nt" style="color: navy;">\end{lstlisting}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC139" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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<td class="diff-line-num new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="tex"><span class="k" style="font-weight: 600;">\noindent</span> Now build and install <span class="k" style="font-weight: 600;">\andi</span>.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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141

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC141" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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142

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="tex"><span class="nt" style="color: navy;">\begin{lstlisting}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="tex">~/andi-0.1<span class="idiff left right">1</span> <span class="c" style="color: #998; font-style: italic;">%  ./configure</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="tex">~/andi-0.1<span class="idiff left right">1</span> <span class="c" style="color: #998; font-style: italic;">%  make</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="tex">~/andi-0.1<span class="idiff left right">1</span> <span class="c" style="color: #998; font-style: italic;">%  sudo make install</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="tex">~/andi-0.1<span class="idiff left right">2</span> <span class="c" style="color: #998; font-style: italic;">%  ./configure</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="tex">~/andi-0.1<span class="idiff left right">2</span> <span class="c" style="color: #998; font-style: italic;">%  make</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="tex">~/andi-0.1<span class="idiff left right">2</span> <span class="c" style="color: #998; font-style: italic;">%  sudo make install</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="tex"><span class="nt" style="color: navy;">\end{lstlisting}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC148" class="line" lang="tex"><span class="k" style="font-weight: 600;">\noindent</span> This installs <span class="k" style="font-weight: 600;">\andi</span> for all users on your system. If you do not have root privileges, you will find a working copy of <span class="k" style="font-weight: 600;">\andi</span> in the <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="nb" style="color: #0086b3;">src</span><span class="p">$</span> subdirectory. For the rest of this documentation, <span class="idiff left right">I will assume</span>, that <span class="k" style="font-weight: 600;">\andi</span> is in your <span class="k" style="font-weight: 600;">\textdollar\lstinline</span>!PATH!.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="tex"><span class="k" style="font-weight: 600;">\noindent</span> This installs <span class="k" style="font-weight: 600;">\andi</span> for all users on your system. If you do not have root privileges, you will find a working copy of <span class="k" style="font-weight: 600;">\andi</span> in the <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="nb" style="color: #0086b3;">src</span><span class="p">$</span> subdirectory. For the rest of this documentation, <span class="idiff left right">it is assumed</span>, that <span class="k" style="font-weight: 600;">\andi</span> is in your <span class="k" style="font-weight: 600;">\textdollar\lstinline</span>!PATH!.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

149

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="tex">Now <span class="k" style="font-weight: 600;">\andi</span> should be ready for use. Try invoking the help.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="tex"><span class="nt" style="color: navy;">\begin{lstlisting}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="tex">~/andi-0.1<span class="idiff left">1 </span><span class="c" style="color: #998; font-style: italic;"><span class="idiff right">%  andi --help</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="tex"><span class="idiff left right">Usage: andi [-jlv] [-b INT] [-p FLOAT] [-m MODEL] [-t INT] FILES..</span>.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="tex">  <span class="idiff left right">FILES... can be any sequence of FASTA files. If no files are supplied, stdin is used instead</span>.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="tex">~/andi-0.1<span class="idiff left">2 </span><span class="c" style="color: #998; font-style: italic;"><span class="idiff right">%  Usage: andi [OPTIONS...] FILES...</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="tex"><span class="idiff left right">  FILES... can be any sequence of FASTA files</span>.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="tex">  <span class="idiff left right">Use '-' as file name to read from stdin</span>.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="tex">Options:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="tex">  -b, --bootstrap<span class="idiff left right"> <INT></span>  Print additional bootstrap matrices</span>

</pre>

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="tex">      --file-of-filenames<span class="idiff left right"> <FILE></span>  Read additional filenames from FILE; one per line</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="tex">  -b, --bootstrap<span class="idiff left right">=INT</span>  Print additional bootstrap matrices</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="tex">      --file-of-filenames<span class="idiff left right">=FILE</span>  Read additional filenames from FILE; one per line</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="tex">  -j, --join           Treat all sequences from one file as a single genome</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="tex">  -l, --low-memory     Use less memory at the cost of speed</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="tex">  -m, --model <Raw|JC|Kimura>  Pick an evolutionary model; default: JC</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="tex">  -p <FLOAT>           Significance of an anchor; default: 0.025</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="tex">  -t, --threads <INT>  Set the number of threads; by default, all available processors are used</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="tex">  -m, --model=MODEL    Pick an evolutionary model of 'Raw', 'JC', 'Kimura'; default: JC</span>

</pre>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="tex">  -p FLOAT             Significance of an anchor; default: 0.025</span>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="tex">      --progress=WHEN  Print a progress bar 'always', 'never', or 'auto'; default: auto</span>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="tex">  -t, --threads=INT    Set the number of threads; by default, all processors are used</span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="tex">      --truncate-names Truncate names to ten characters</span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="tex">  -v, --verbose        Prints additional information</span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="tex">  -h, --help           Display this help and exit</span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -230,9 +231,9 @@ When the \algo{join} mode is active, the file names are used to label the indivi</td>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="tex">If not enough file names are provided, <span class="k" style="font-weight: 600;">\andi</span> will try to read sequences from the standard input stream. This behaviour can be explicitly triggered by passing a single dash (<span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="o" style="font-weight: 600;">-</span><span class="p">$</span>) as a file name, which is useful in pipelines.</span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="tex">If <span class="k" style="font-weight: 600;">\andi</span> seems to take unusually long, or requires huge amounts of memory, then you might have forgotten the <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>join<span class="p">}</span> switch. This makes <span class="k" style="font-weight: 600;">\andi</span> compare each contig instead of each genome, resulting in many more comparisons! <span class="idiff left">To make </span><span class="k" style="font-weight: 600;"><span class="idiff">\andi</span></span><span class="idiff"> output the number of genome it about to compare, use the </span><span class="k" style="font-weight: 600;"><span class="idiff">\lstinline</span></span><span class="p"><span class="idiff">$</span></span><span class="o" style="font-weight: 600;"><span class="idiff">--</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">verbose</span></span><span class="p"><span class="idiff">$</span></span><span class="idiff right"> switch</span>.</span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="tex">If <span class="k" style="font-weight: 600;">\andi</span> seems to take unusually long, or requires huge amounts of memory, then you might have forgotten the <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>join<span class="p">}</span> switch. This makes <span class="k" style="font-weight: 600;">\andi</span> compare each contig instead of each genome, resulting in many more comparisons! <span class="idiff left">Since version 0.12 </span><span class="k" style="font-weight: 600;"><span class="idiff">\andi</span></span><span class="idiff"> produces a progressmeter on the standard error stream. </span><span class="k" style="font-weight: 600;"><span class="idiff">\andi</span></span><span class="idiff"> tries to be smart about when to show or hide the progress bar. You can manually change this behaviour using the </span><span class="k" style="font-weight: 600;"><span class="idiff">\lstinline</span></span><span class="idiff right">!--progress! option</span>.</span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="tex">Starting with version 0.11 <span class="k" style="font-weight: 600;">\andi</span> supports an extra way of input. Instead of passing file names directly to <span class="k" style="font-weight: 600;">\andi</span> via the commandline arguments, the file<span class="idiff left">s may also be read from a file itself. Using this new </span><span class="k" style="font-weight: 600;"><span class="idiff">\lstinline</span></span><span class="p"><span class="idiff">$</span></span><span class="o" style="font-weight: 600;"><span class="idiff">--</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">of</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">filenames</span></span><span class="p"><span class="idiff right">$</span></span> can work around limitations imposed be the shell.</span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="tex">Starting with version 0.11 <span class="k" style="font-weight: 600;">\andi</span> supports an extra way of input. Instead of passing file names directly to <span class="k" style="font-weight: 600;">\andi</span> via the commandline arguments, the file<span class="idiff left"> names may also be read from a file itself. Using this new </span><span class="k" style="font-weight: 600;"><span class="idiff">\lstinline</span></span><span class="p"><span class="idiff">$</span></span><span class="o" style="font-weight: 600;"><span class="idiff">--</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">of</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">filenames</span></span><span class="p"><span class="idiff">$</span></span><span class="idiff right"> argument</span> can work around limitations imposed be the shell.</span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="tex">The following three snippets have the same functionality.</span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="tex"></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -267,7 +268,7 @@ If the computation completed successfully, \andi exits with the status code 0. O</td>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="tex"><span class="k" style="font-weight: 600;">\section</span><span class="p">{</span>Options<span class="p">}</span> <span class="k" style="font-weight: 600;">\label</span><span class="p">{</span>sec:options<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="tex"><span class="k" style="font-weight: 600;">\andi</span> takes a small number of commandline options, of which even fewer are of interest on a day-to-day basis. If <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="nb" style="color: #0086b3;">andi </span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">h</span><span class="p">$</span> displays a <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">t</span><span class="p">$</span> option, then <span class="k" style="font-weight: 600;">\andi</span> was compiled with multi-threading support (implemented using <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>OpenMP<span class="p">}</span>). By default <span class="k" style="font-weight: 600;">\andi</span> uses all available processors. However, to restrict the number of threads, use <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">t</span><span class="p">$</span>.</span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="tex"><span class="k" style="font-weight: 600;">\andi</span> takes a small number of commandline options, of which even fewer are of interest on a day-to-day basis. If <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="nb" style="color: #0086b3;">andi </span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">h</span><span class="p">$</span> displays a <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">t</span><span class="p">$</span> option, then <span class="k" style="font-weight: 600;">\andi</span> was compiled with multi-threading support (implemented using <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>OpenMP<span class="p">}</span>). By default<span class="idiff left right">,</span> <span class="k" style="font-weight: 600;">\andi</span> uses all available processors. However, to restrict the number of threads, use <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">t</span><span class="p">$</span>.</span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="tex"><span class="nt" style="color: navy;">\begin{lstlisting}</span></span>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="tex">~ <span class="c" style="color: #998; font-style: italic;">%  time andi ../test/1M.1.fasta -t 1</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -298,13 +299,13 @@ S1        0.0000 0.1071</td>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="tex">S2        0.1071 0.0000</span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="tex"><span class="nt" style="color: navy;">\end{lstlisting}</span></span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="tex">The original <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>phylip<span class="p">}</span> only supports distance matrices with names no longer than ten characters. However, this sometimes leads to problems with long accession numbers. Starting with version 0.11 <span class="k" style="font-weight: 600;">\andi</span> print the full name of a sequence, even if it is longer than ten characters. If your downstream tools have trouble with this, use <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="o" style="font-weight: 600;">--</span><span class="nb" style="color: #0086b3;">truncate</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">names</span><span class="p">$</span> to reimpose the limit.</span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="tex">The original <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>phylip<span class="p">}</span> only supports distance matrices with names no longer than ten characters. However, this sometimes leads to problems with long accession numbers. Starting with version 0.11 <span class="k" style="font-weight: 600;">\andi</span> print<span class="idiff left right">s</span> the full name of a sequence, even if it is longer than ten characters. If your downstream tools have trouble with this, use <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="o" style="font-weight: 600;">--</span><span class="nb" style="color: #0086b3;">truncate</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">names</span><span class="p">$</span> to reimpose the limit.</span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="tex">Also new in version 0.11 is the <span class="k" style="font-weight: 600;">\lstinline</span><span class="p">$</span><span class="o" style="font-weight: 600;">--</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">of</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">filenames</span><span class="p">$</span> option. See Section~<span class="k" style="font-weight: 600;">\ref</span><span class="p">{</span>sec:join<span class="p">}</span> for details.</span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="tex"><span class="k" style="font-weight: 600;">\section</span><span class="p">{</span>Example: <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>eco29<span class="p">}}</span></span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="tex">Here follows a real-world example of how to use <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>andi<span class="p">}</span>. It makes heavy use of the commandline and tools like <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>Phylip<span class="p">}</span>. If you prefer <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>R<span class="p">}</span>, check out this excellent <span class="k" style="font-weight: 600;"><span class="idiff left">\href</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">http://holtlab.net/2015/05/08/r-code-to-infer-tree-from-andi-output/</span><span class="p"><span class="idiff">}{</span></span><span class="idiff">blog post</span><span class="p"><span class="idiff">}</span></span><span class="idiff right"> by Kathryn Holt.</span></span>

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="tex">Here follows a real-world example of how to use <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>andi<span class="p">}</span>. It makes heavy use of the commandline and tools like <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>Phylip<span class="p">}</span>. If you prefer <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>R<span class="p">}</span>, check out this excellent <span class="idiff left">blog post by Kathryn Holt.</span><span class="k" style="font-weight: 600;"><span class="idiff">\footnote</span></span><span class="p"><span class="idiff">{</span></span><span class="k" style="font-weight: 600;"><span class="idiff">\url</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">http://holtlab.net/2015/05/08/r-code-to-infer-tree-from-andi-output/</span><span class="p"><span class="idiff right">}}</span></span></span>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="tex">As a data set we use <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>eco29<span class="p">}</span>; 29 genomes of <span class="k" style="font-weight: 600;">\textit</span><span class="p">{</span>E. Coli<span class="p">}</span> and <span class="k" style="font-weight: 600;">\textit</span><span class="p">{</span>Shigella<span class="p">}</span>. You can download the data from here: <span class="p">{</span><span class="k" style="font-weight: 600;">\small</span><span class="p">{</span><span class="k" style="font-weight: 600;">\url</span><span class="p">{</span>http://guanine.evolbio.mpg.de/andi/eco29.fasta.gz<span class="p">}}}</span>. The genomes have an average length of 4.9~million nucleotides amounting to a total <span class="k" style="font-weight: 600;">\SI</span><span class="p">{</span>138<span class="p">}{</span><span class="k" style="font-weight: 600;">\mega\byte</span><span class="p">}</span>.</span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="tex"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -414,11 +415,11 @@ Some command line parameters of \andi require arguments. If these are not of the</td>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="tex"><span class="k" style="font-weight: 600;">\section</span><span class="p">{</span>Output-related Warnings<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="tex">As the input sequences get more evolutionary divergent, <span class="k" style="font-weight: 600;">\andi</span> finds less anchors. With less anchors, less nucleotides are considered homologous between two sequences. If no anchors are found, comparison fails and <span class="k" style="font-weight: 600;">\lstinline</span>!nan! is printed instead. See our paper and especially Figure~2 for details.</span>

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="tex">As the input sequences get more evolutionary divergent, <span class="k" style="font-weight: 600;">\andi</span> finds less <span class="idiff left right">homologous </span>anchors. With less anchors, less nucleotides are considered homologous between two sequences. If no anchors are found, comparison fails and <span class="k" style="font-weight: 600;">\lstinline</span>!nan! is printed instead. See our paper and especially Figure~2 for details.</span>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="tex"><span class="k" style="font-weight: 600;">\subsection*</span><span class="p">{</span>NaN<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC421" class="line" lang="tex">No <span class="idiff left right">anchor</span>s were found. Your sequences are very divergent (<span class="p">$</span><span class="nb" style="color: #0086b3;">d></span><span class="m" style="color: #099;">0</span><span class="nb" style="color: #0086b3;">.</span><span class="m" style="color: #099;">5</span><span class="p">$</span>) or sprout a lot of indels that make comparison difficult.</span>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="tex">No <span class="idiff left right">homologous section</span>s were found. Your sequences are very divergent (<span class="p">$</span><span class="nb" style="color: #0086b3;">d></span><span class="m" style="color: #099;">0</span><span class="nb" style="color: #0086b3;">.</span><span class="m" style="color: #099;">5</span><span class="p">$</span>) or sprout a lot of indels that make comparison difficult.</span>

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="tex"><span class="k" style="font-weight: 600;">\subsection*</span><span class="p">{</span>Little Homology<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="tex"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -469,7 +470,7 @@ The unit tests are located in the \andi repository under the \lstinline$./test$ </td>

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<pre style="margin: 0;"> <span id="LC470" class="line" lang="tex">~/andi <span class="c" style="color: #998; font-style: italic;">%   make check</span></span>

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="tex"><span class="nt" style="color: navy;">\end{lstlisting}</span></span>

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC472" class="line" lang="tex"><span class="k" style="font-weight: 600;">\noindent</span> The unit tests are also checked each time a commit is sent to the repository. This is done via <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>TravisCI<span class="p">}</span>.<span class="k" style="font-weight: 600;">\footnote</span><span class="p">{</span><span class="k" style="font-weight: 600;">\url</span><span class="p">{</span>https://travis-ci.org/EvolBioInf/andi<span class="p">}}</span> Thus, a warning is produced, when the builds fail, or the unit tests <span class="idiff left">to not run successfully. Currently, the unit tests cover more than 75</span><span class="k" style="font-weight: 600;"><span class="idiff">\%</span></span><span class="idiff"> of the code. This is computed via the </span><span class="k" style="font-weight: 600;"><span class="idiff">\algo</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">Travis</span><span class="p"><span class="idiff">}</span></span><span class="idiff"> builds and a service called </span><span class="k" style="font-weight: 600;"><span class="idiff">\algo</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">Coveralls</span><span class="p"><span class="idiff">}</span></span><span class="idiff">.</span><span class="k" style="font-weight: 600;"><span class="idiff">\footnote</span></span><span class="p"><span class="idiff">{</span></span><span class="k" style="font-weight: 600;"><span class="idiff">\url</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">https://coveralls.io/r/EvolBioInf/andi</span><span class="p"><span class="idiff">}}</span></span><span class="idiff right"> Unfortunately, coveralls is broken at this point in time.</span></span>

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="tex"><span class="k" style="font-weight: 600;">\noindent</span> The unit tests are also checked each time a commit is sent to the repository. This is done via <span class="k" style="font-weight: 600;">\algo</span><span class="p">{</span>TravisCI<span class="p">}</span>.<span class="k" style="font-weight: 600;">\footnote</span><span class="p">{</span><span class="k" style="font-weight: 600;">\url</span><span class="p">{</span>https://travis-ci.org/EvolBioInf/andi<span class="p">}}</span> Thus, a warning is produced, when the builds fail, or the unit tests <span class="idiff left">did not run successfully. Currently, the unit tests cover more than 75</span><span class="k" style="font-weight: 600;"><span class="idiff">\%</span></span><span class="idiff"> of the code. This is computed via the </span><span class="k" style="font-weight: 600;"><span class="idiff">\algo</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">Travis</span><span class="p"><span class="idiff">}</span></span><span class="idiff"> builds and a service called </span><span class="k" style="font-weight: 600;"><span class="idiff">\algo</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">Coveralls</span><span class="p"><span class="idiff">}</span></span><span class="idiff">.</span><span class="k" style="font-weight: 600;"><span class="idiff">\footnote</span></span><span class="p"><span class="idiff">{</span></span><span class="k" style="font-weight: 600;"><span class="idiff">\url</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff">https://coveralls.io/r/EvolBioInf/andi</span><span class="p"><span class="idiff right">}}</span></span></span>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC475" class="line" lang="tex"><span class="k" style="font-weight: 600;">\section</span><span class="p">{</span>Known Issues<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC476" class="line" lang="tex"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,6 +27,7 @@ args+=(</td>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">             Kimura\:Kimura\-two\-parameter</span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">     ))'</span>

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29

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29

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">     "($info)-p+[Significance of an anchor; default\: 0.025]:float:"</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">     "($info)--progress=[Show progress bar]:when:(always auto never)"</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

30

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">     "($info -t --threads)"{-t+,--threads=}'[The number of threads to be used; by default, all available processors are used]:num_threads:'</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">     "($info)--truncate-names[Print only the first ten characters of each name]"</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">     "($info)*"{-v,--verbose}'[Prints additional information]'</span>

</pre>

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<br>

</li>

<li id="e4121eb35479a00bb2becf6c512563545bb34482">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#e4121eb35479a00bb2becf6c512563545bb34482"><strong>src/andi.c</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,10 +45,9 @@</td>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">FLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">THREADS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">BOOTSTRAP</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left right">RANDOM_ANCHOR_PROP</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">025</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left right">ANCHOR_P_VALUE</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">025</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"><span class="n" style="color: #333;">gsl_rng</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">RNG</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M_JC</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">EXIT_CODE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">usage</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">version</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,6 +65,7 @@ int main(int argc, char *argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c">             <span class="p">{</span><span class="s" style="color: #d14;">"version"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c">             <span class="p">{</span><span class="s" style="color: #d14;">"truncate-names"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c">             <span class="p">{</span><span class="s" style="color: #d14;">"file-of-filenames"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c">             <span class="p">{</span><span class="s" style="color: #d14;">"progress"</span><span class="p">,</span> <span class="n" style="color: #333;">optional_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span></span>

</pre>

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69

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<td class="diff-line-num new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c">             <span class="p">{</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">},</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c">             <span class="p">{</span><span class="s" style="color: #d14;">"verbose"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'v'</span><span class="p">},</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c">             <span class="p">{</span><span class="s" style="color: #d14;">"join"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'j'</span><span class="p">},</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -79,6 +79,9 @@ int main(int argc, char *argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c">     <span class="c1" style="color: #998; font-style: italic;">// Use all available processors by default.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c">     <span class="n" style="color: #333;">THREADS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">omp_get_num_procs</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c">     <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">P_AUTO</span><span class="p">,</span> <span class="n" style="color: #333;">P_NEVER</span><span class="p">,</span> <span class="n" style="color: #333;">P_ALWAYS</span> <span class="p">}</span> <span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P_AUTO</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c">     <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">string_vector</span> <span class="n" style="color: #333;">file_names</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c">     <span class="n" style="color: #333;">string_vector_init</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">file_names</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -105,6 +108,19 @@ int main(int argc, char *argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcasecmp</span><span class="p">(</span><span class="n" style="color: #333;">option_str</span><span class="p">,</span> <span class="s" style="color: #d14;">"file-of-filenames"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

106

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c">                                    <span class="n" style="color: #333;">read_into_string_vector</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">file_names</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

111

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC111" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcasecmp</span><span class="p">(</span><span class="n" style="color: #333;">option_str</span><span class="p">,</span> <span class="s" style="color: #d14;">"progress"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

112

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC112" class="line" lang="c">                                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">optarg</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">strcasecmp</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="s" style="color: #d14;">"always"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

113

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c">                                            <span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P_ALWAYS</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c">                                    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcasecmp</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c">                                            <span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P_AUTO</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

116

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c">                                    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcasecmp</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="s" style="color: #d14;">"never"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c">                                            <span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P_NEVER</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

118

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC118" class="line" lang="c">                                    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

119

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC119" class="line" lang="c">                                            <span class="n" style="color: #333;">warnx</span><span class="p">(</span><span class="s" style="color: #d14;">"invalid argument to --progress '%s'. Expected "</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

120

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC120" class="line" lang="c">                                                      <span class="s" style="color: #d14;">"one of 'auto', 'always', or 'never'."</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

121

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC121" class="line" lang="c">                                                      <span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

122

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC122" class="line" lang="c">                                    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

123

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC123" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

108

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<td class="diff-line-num new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

124

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC124" class="line" lang="c">                            <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

109

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<td class="diff-line-num new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

125

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC125" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">:</span> <span class="n" style="color: #333;">usage</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -117,21 +133,21 @@ int main(int argc, char *argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c">                            <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">prop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtod</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"></span>

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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">optarg</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="c">                                    <span class="n" style="color: #333;"><span class="idiff left right">warn</span>x</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c">                                    <span class="n" style="color: #333;"><span class="idiff left right">soft_err</span>x</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="c">                                            <span class="s" style="color: #d14;">"Expected a floating point number for -p argument, but "</span></span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c">                                            <span class="s" style="color: #d14;">"'%s' was given. Skipping argument."</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c">                                            <span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c">                                    <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c">                            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c"></span>

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<td class="diff-line-num old old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prop</span> <span class="o" style="font-weight: 600;"><</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">prop</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">></span></span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="c">                                    <span class="n" style="color: #333;"><span class="idiff left">warnx</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"A probability should be a value between 0 and 1;</span> "</span></span>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="c">                                            <span class="idiff left">  </span><span class="s" style="color: #d14;"><span class="idiff right">"</span>Ignoring -p %f argument."</span><span class="p">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="c">                                              <span class="n" style="color: #333;">prop</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prop</span> <span class="o" style="font-weight: 600;"><<span class="idiff left">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">prop</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">>=</span></span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c">                                    <span class="n" style="color: #333;"><span class="idiff left">soft_errx</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"A probability should be a value between 0 and</span> "</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c">                                            <span class="idiff left">         </span><span class="s" style="color: #d14;"><span class="idiff right">"1, exlusive; </span>Ignoring -p %f argument."</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c">                                            <span class="idiff left right"> </span>  <span class="n" style="color: #333;">prop</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c">                                    <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c">                            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="c">                            <span class="n" style="color: #333;"><span class="idiff left right">RANDOM_ANCHOR_PROP</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prop</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c">                            <span class="n" style="color: #333;"><span class="idiff left right">ANCHOR_P_VALUE</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prop</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c">                            <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c">                    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'l'</span><span class="p">:</span> <span class="n" style="color: #333;">FLAGS</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">F_LOW_MEMORY</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -172,7 +188,7 @@ int main(int argc, char *argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="c">                            <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bootstrap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtoul</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">optarg</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">bootstrap</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="c">                                    <span class="n" style="color: #333;"><span class="idiff left right">warn</span>x</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="c">                                    <span class="n" style="color: #333;"><span class="idiff left right">soft_err</span>x</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="c">                                            <span class="s" style="color: #d14;">"Expected a positive number for -b argument, but '%s' "</span></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c">                                            <span class="s" style="color: #d14;">"was given. Ignoring -b argument."</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="c">                                            <span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -191,8 +207,9 @@ int main(int argc, char *argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c">                            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcasecmp</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="s" style="color: #d14;">"KIMURA"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="c">                                    <span class="n" style="color: #333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M_KIMURA</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c">                            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="c">                                    <span class="n" style="color: #333;">warnx</span><span class="p">(</span><span class="s" style="color: #d14;">"Ignoring argument for --model. Expected Raw, JC or "</span></span>

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<pre style="margin: 0;">-<span id="LC195" class="line" lang="c">                                              <span class="s" style="color: #d14;">"Kimura"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="c">                                    <span class="n" style="color: #333;">soft_errx</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c">                                            <span class="s" style="color: #d14;">"Ignoring argument for --model. Expected Raw, JC or "</span></span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="c">                                            <span class="s" style="color: #d14;">"Kimura"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c">                            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="c">                            <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="c">                    <span class="p">}</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -217,11 +234,13 @@ int main(int argc, char *argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">minfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FLAGS</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">F_JOIN</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">string_vector_size</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">file_names</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">minfiles</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// not enough files passed via arguments; read from stdin.</span></span>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="c">            <span class="n" style="color: #333;">string_vector_push_back</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">file_names</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// explain to the user, why nothing is happening.</span></span>

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<td class="diff-line-num new_line old" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isatty</span><span class="p">(</span><span class="n" style="color: #333;">STDIN_FILENO</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="c">                    <span class="n" style="color: #333;">warnx</span><span class="p">(</span><span class="s" style="color: #d14;">"Not enough file names given; expecting input via stdin."</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// not enough files passed via arguments</span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isatty</span><span class="p">(</span><span class="n" style="color: #333;">STDIN_FILENO</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="c">                    <span class="c1" style="color: #998; font-style: italic;">// read from stdin in pipe</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="c">                    <span class="n" style="color: #333;">string_vector_push_back</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">file_names</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="c">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="c">                    <span class="c1" style="color: #998; font-style: italic;">// print a helpful message on './andi' without args</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c">                    <span class="n" style="color: #333;">usage</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -248,11 +267,6 @@ int main(int argc, char *argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c">                     <span class="n" style="color: #333;">n</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">FLAGS</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">F_VERBOSE</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="c">            <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Comparing %zu sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC253" class="line" lang="c">            <span class="n" style="color: #333;">fflush</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c">    <span class="n" style="color: #333;">RNG</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gsl_rng_alloc</span><span class="p">(</span><span class="n" style="color: #333;">gsl_rng_default</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">RNG</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="c">            <span class="n" style="color: #333;">err</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"RNG allocation failed."</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -293,20 +307,27 @@ int main(int argc, char *argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">FLAGS</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">F_SHORT</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="c">            <span class="n" style="color: #333;">warnx</span><span class="p">(</span><span class="s" style="color: #d14;">"One of the given input sequences is shorter than a thousand "</span></span>

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="c">                      <span class="s" style="color: #d14;">"nucleotides. This may result in inaccurate distances. Try an "</span></span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="c">                      <span class="s" style="color: #d14;">"alignment instead."</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="c">            <span class="n" style="color: #333;">soft_errx</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="c">                    <span class="s" style="color: #d14;">"One of the given input sequences is shorter than a thousand "</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="c">                    <span class="s" style="color: #d14;">"nucleotides. This may result in inaccurate distances. Try an "</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="c">                    <span class="s" style="color: #d14;">"alignment instead."</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// side channel</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

302

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<td class="diff-line-num new_line old" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="c">    <span class="n" style="color: #333;">EXIT_CODE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// determine whether to print a progress bar</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">P_AUTO</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="c">            <span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isatty</span><span class="p">(</span><span class="n" style="color: #333;">STDERR_FILENO</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">P_ALWAYS</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">P_NEVER</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">P_ALWAYS</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

321

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="c">            <span class="n" style="color: #333;">FLAGS</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">F_PRINT_PROGRESS</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

322

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

323

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC323" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

304

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<td class="diff-line-num new_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC324" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// compute distance matrix</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

305

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<td class="diff-line-num new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

325

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="c">    <span class="n" style="color: #333;">calculate_distances</span><span class="p">(</span><span class="n" style="color: #333;">dsa_data</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dsa</span><span class="p">),</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

326

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC326" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

327

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC327" class="line" lang="c">    <span class="n" style="color: #333;">dsa_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dsa</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC328" class="line" lang="c">    <span class="n" style="color: #333;">gsl_rng_free</span><span class="p">(</span><span class="n" style="color: #333;">RNG</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_CODE</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC329" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">FLAGS</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">F_SOFT_ERROR</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">EXIT_FAILURE</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -314,22 +335,25 @@ int main(int argc, char *argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<td class="diff-line-num old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">usage</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">status</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="c">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">str</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC317" class="line" lang="c">            <span class="s" style="color: #d14;">"Usage: andi [<span class="idiff left right">-jlv] [-b INT] [-p FLOAT] [-m MODEL] [-t INT</span>] FILES...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<td class="diff-line-num new_line old" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC318" class="line" lang="c">            <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">FILES... can be any sequence of FASTA files.<span class="idiff left right"> If no files are </span>"</span></span>

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<td class="diff-line-num old old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC319" class="line" lang="c">            <span class="s" style="color: #d14;">"<span class="idiff left right">supplied, stdin is used instead</span>.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="c">            <span class="s" style="color: #d14;">"Usage: andi [<span class="idiff left right">OPTIONS...</span>] FILES...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<td class="diff-line-num new old_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="c">            <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">FILES... can be any sequence of FASTA files.</span><span class="se" style="color: #d14;"><span class="idiff left right">\n</span></span><span class="s" style="color: #d14;">"</span></span>

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<td class="diff-line-num new old_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="c">            <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;"><span class="idiff left">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">Use '-' as file name to read from stdin</span>.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="c">            <span class="s" style="color: #d14;">"Options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<td class="diff-line-num new_line old" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="c">            <span class="s" style="color: #d14;">"  -b, --bootstrap<span class="idiff left right"> <INT></span>  Print additional bootstrap matrices</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC322" class="line" lang="c">            <span class="s" style="color: #d14;">"      --file-of-filenames<span class="idiff left right"> <FILE></span>  Read additional filenames from "</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="c">            <span class="s" style="color: #d14;">"  -b, --bootstrap<span class="idiff left right">=INT</span>  Print additional bootstrap matrices</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="c">            <span class="s" style="color: #d14;">"      --file-of-filenames<span class="idiff left right">=FILE</span>  Read additional filenames from "</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="c">            <span class="s" style="color: #d14;">"FILE; one per line</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="c">            <span class="s" style="color: #d14;">"  -j, --join           Treat all sequences from one file as a single "</span></span>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="c">            <span class="s" style="color: #d14;">"genome</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="c">            <span class="s" style="color: #d14;">"  -l, --low-memory     Use less memory at the cost of speed</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC327" class="line" lang="c">            <span class="s" style="color: #d14;">"  -m, --model <Raw|JC|Kimura>  Pick an evolutionary model; default: "</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC348" class="line" lang="c">            <span class="s" style="color: #d14;">"  -m, --model=MODEL    Pick an evolutionary model of 'Raw', 'JC', "</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="c">            <span class="s" style="color: #d14;">"'Kimura'; default: "</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="c">            <span class="s" style="color: #d14;">"JC</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="c">            <span class="s" style="color: #d14;">"  -p <FLOAT>           Significance of an anchor; default: 0.025</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="c">            <span class="s" style="color: #d14;">"  -p FLOAT             Significance of an anchor; default: 0.025</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="c">            <span class="s" style="color: #d14;">"      --progress=WHEN  Print a progress bar 'always', 'never', or "</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="c">            <span class="s" style="color: #d14;">"'auto'; default: auto</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _OPENMP</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="c">            <span class="s" style="color: #d14;">"  -t, --threads<span class="idiff left right"> <INT></span>  Set the number of threads; by default, all "</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="c">            <span class="s" style="color: #d14;">"<span class="idiff left right">available </span>processors are used</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC355" class="line" lang="c">            <span class="s" style="color: #d14;">"  -t, --threads<span class="idiff left right">=INT  </span>  Set the number of threads; by default, all "</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="c">            <span class="s" style="color: #d14;">"processors are used</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="c">            <span class="s" style="color: #d14;">"      --truncate-names Truncate names to ten characters</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC359" class="line" lang="c">            <span class="s" style="color: #d14;">"  -v, --verbose        Prints additional information</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<br>

</li>

<li id="e611a4867dd9a0b53115c8847a0302431c5da23d">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#e611a4867dd9a0b53115c8847a0302431c5da23d"><strong>src/dist_hack.h</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,9 +2,10 @@</td>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @brief This file is a preprocessor hack for the two functions `distMatrix`</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * and `distMatrixLM`.</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// clang-format off</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef FAST</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define NAME distMatrix</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define P_OUTER _Pragma("omp parallel for num_threads( THREADS)")</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define P_OUTER _Pragma("omp parallel for num_threads( THREADS)<span class="idiff left right"> default(none) shared(progress_counter) firstprivate( stderr, M, sequences, n, print_progress)</span>")</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define P_INNER</span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#undef NAME</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#undef P_INNER</span></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define NAME distMatrixLM</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define P_OUTER</span></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define P_INNER _Pragma("omp parallel for num_threads( THREADS)")</span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define P_INNER _Pragma("omp parallel for num_threads( THREADS)<span class="idiff left right"> default(none) shared(progress_counter) firstprivate( stderr, M, sequences, n, print_progress, i, E, subject)</span>")</span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// clang-format on</span></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** @brief This function calls dist_andi for pairs of subjects and queries, and</span></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * thereby fills the distance matrix.</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,6 +34,14 @@</td>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">NAME</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">seq_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sequences</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">progress_counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FLAGS</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">F_PRINT_PROGRESS</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"></span>

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<td class="diff-line-num new old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c">     <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">print_progress</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c">             <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Comparing %zu sequences: %5.1f%% (%zu/%zu)"</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c">                             <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c">     <span class="p">}</span></span>

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<td class="diff-line-num new old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c">     <span class="c1" style="color: #998; font-style: italic;">//#pragma</span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c">     <span class="n" style="color: #333;">P_OUTER</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c">     <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,15 +66,31 @@ void NAME(struct model *M, const seq_t *sequences, size_t n) {</td>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c">                     <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">ql</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c">                     <span class="n" style="color: #333;">M</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dist_anchor</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">E</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">S</span><span class="p">,</span> <span class="n" style="color: #333;">ql</span><span class="p">,</span> <span class="n" style="color: #333;">subject</span><span class="p">.</span><span class="n" style="color: #333;">gc</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#pragma omp atomic update</span></span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c">                     <span class="n" style="color: #333;">progress_counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c">             <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="c">             <span class="c1" style="color: #998; font-style: italic;">// TODO: Provide a nicer progress indicator.</span></span>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c">             <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">FLAGS</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">F_EXTRA_VERBOSE</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c">             <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">print_progress</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c">                     <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">local_progress_counter</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c">                     <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">num_comparisons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#pragma omp atomic read</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c">                     <span class="n" style="color: #333;">local_progress_counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">progress_counter</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c">                     <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

82

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC82" class="line" lang="c">                             <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">local_progress_counter</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">num_comparisons</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

83

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<td class="diff-line-num new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

84

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#pragma omp critical</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

64

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<td class="diff-line-num new_line old" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC64" class="line" lang="c">                     <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Subject %s done.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c">                     <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">Comparing %zu sequences: %5.1f%% (%zu/%zu)"</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c">                                     <span class="n" style="color: #333;">progress</span><span class="p">,</span> <span class="n" style="color: #333;">local_progress_counter</span><span class="p">,</span> <span class="n" style="color: #333;">num_comparisons</span><span class="p">);</span></span>

</pre>

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65

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<td class="diff-line-num new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

87

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c">             <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC88" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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<td class="diff-line-num new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c">             <span class="n" style="color: #333;">esa_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">E</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c">             <span class="n" style="color: #333;">seq_subject_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">subject</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

69

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<td class="diff-line-num new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

91

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c">     <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

92

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

93

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC93" class="line" lang="c">     <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">print_progress</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c">             <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">", done.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

95

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC95" class="line" lang="c">     <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

70

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<td class="diff-line-num new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="010ebeab960fdcf8c02bab9f78bc704a379c3490">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#010ebeab960fdcf8c02bab9f78bc704a379c3490"><strong>src/esa.c</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -313,7 +313,9 @@ int esa_init_CLD(esa_s *C) {</td>

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<td class="diff-line-num new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="c">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">saidx_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">LCP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">LCP</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="c">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">pair_s</span> <span class="p">{</span> <span class="n" style="color: #333;">saidx_t</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">lcp</span><span class="p">;</span> <span class="p">}</span> <span class="n" style="color: #333;">pair_t</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="c">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">pair_s</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="c">            <span class="n" style="color: #333;">saidx_t</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">lcp</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="c">    <span class="p">}</span> <span class="n" style="color: #333;">pair_t</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="c">    <span class="n" style="color: #333;">pair_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">stack</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">((</span><span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">stack</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="c">    <span class="n" style="color: #333;">CHECK_MALLOC</span><span class="p">(</span><span class="n" style="color: #333;">stack</span><span class="p">);</span></span>

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<br>

</li>

<li id="c30c220576b993ebc2341d565eb0ff0c4a10da82">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#c30c220576b993ebc2341d565eb0ff0c4a10da82"><strong>src/global.h</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,11 +26,11 @@ extern int FLAGS;</td>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">THREADS</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * The ::<span class="idiff left right">RANDOM_ANCHOR_PROP represents the probability with which a found</span></span></span>

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<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">anchor is a random match and not homologous. Its value can be set using</span></span></span>

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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * the `-p` switch.</span></span>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * The ::<span class="idiff left right">ANCHOR_P_VALUE represents the probability that an anchor will be found,</span></span></span>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">if the two sequences are unrelated. I.e. it is the p-value for H_0: random</span></span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">sequences. Its value can be set using </span>the `-p` switch.</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left right">RANDOM_ANCHOR_PROP</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left right">ANCHOR_P_VALUE</span></span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * The number of matrices that should be bootstrapped.</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,11 +50,6 @@ extern int MODEL;</td>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"><span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">M_RAW</span><span class="p">,</span> <span class="n" style="color: #333;">M_JC</span><span class="p">,</span> <span class="n" style="color: #333;">M_KIMURA</span> <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Global exit code. Should be non-zero on error.</span></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">EXIT_CODE</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This enum contains the available flags. Please note that all</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * available options are a power of 2.</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,7 +61,9 @@ enum {</td>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c">     <span class="n" style="color: #333;">F_NON_ACGT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c">     <span class="n" style="color: #333;">F_JOIN</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c">     <span class="n" style="color: #333;">F_LOW_MEMORY</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">32</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c">     <span class="n" style="color: #333;">F_SHORT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">64</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c">     <span class="n" style="color: #333;">F_SHORT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">64</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c">     <span class="n" style="color: #333;">F_PRINT_PROGRESS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">128</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c">     <span class="n" style="color: #333;">F_SOFT_ERROR</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">256</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -79,6 +76,26 @@ enum {</td>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">           if (PTR == NULL) {                                                     \</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">                   err(errno, "Out of memory");                                       \</span></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">           }                                                                      \</span></span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">   } while (0);</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">   } while (0)</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @brief This macro is used to print a warning and make the program exit with</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * an failure exit code, later.</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define soft_err(...)                                                          \</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">   do {                                                                       \</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">           FLAGS |= F_SOFT_ERROR;                                                 \</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">           warn(__VA_ARGS__);                                                     \</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

89

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">   } while (0)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @brief This macro is used to print a warning and make the program exit with</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * an failure exit code, later.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define soft_errx(...)                                                         \</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">   do {                                                                       \</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">           FLAGS |= F_SOFT_ERROR;                                                 \</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">           warnx(__VA_ARGS__);                                                    \</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">   } while (0)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>

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<br>

</li>

<li id="0f3044ba93433ecc1c927c85984cb8dc55b76b9f">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#0f3044ba93433ecc1c927c85984cb8dc55b76b9f"><strong>src/io.c</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,7 +103,8 @@ size_t string_vector_size(const struct string_vector *sv) {</td>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">read_into_string_vector</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">file_name</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">string_vector</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sv</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">stdin</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">file</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

106

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC106" class="line" lang="c">            <span class="n" style="color: #333;">err</span><span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">file_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c">            <span class="n" style="color: #333;">soft_err</span><span class="p">(</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">file_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

107

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c">            <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

108

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

109

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<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,7 +119,8 @@ void read_into_string_vector(const char *file_name, struct string_vector *sv) {</td>

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<td class="diff-line-num old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

118

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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

119

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

120

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

120

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<td class="diff-line-num new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

121

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

121

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<td class="diff-line-num new_line old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC121" class="line" lang="c">                    <span class="n" style="color: #333;">err</span><span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">file_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

122

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC122" class="line" lang="c">                    <span class="n" style="color: #333;">soft_err</span><span class="p">(</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">file_name</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

123

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC123" class="line" lang="c">                    <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

122

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<td class="diff-line-num new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

123

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<td class="diff-line-num new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

125

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strchr</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -137,7 +139,7 @@ void read_into_string_vector(const char *file_name, struct string_vector *sv) {</td>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

137

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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

138

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<td class="diff-line-num new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">check</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

140

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<td class="diff-line-num new_line old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="c">            <span class="n" style="color: #333;"><span class="idiff left">err</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">errno</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">file_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c">            <span class="n" style="color: #333;"><span class="idiff left">soft_err</span></span><span class="p"><span class="idiff right">(</span></span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">file_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

142

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<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

145

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -198,7 +200,7 @@ void read_fasta(const char *file_name, dsa_t *dsa) {</td>

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<td class="diff-line-num old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

200

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c">            <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">,</span> <span class="n" style="color: #333;">O_RDONLY</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">STDIN_FILENO</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

201

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

202

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">file_descriptor</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC201" class="line" lang="c">            <span class="n" style="color: #333;"><span class="idiff left right">warn</span></span><span class="p">(</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">file_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="c">            <span class="n" style="color: #333;"><span class="idiff left right">soft_err</span></span><span class="p">(</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">file_name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

202

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<td class="diff-line-num new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

204

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c">            <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -209,7 +211,7 @@ void read_fasta(const char *file_name, dsa_t *dsa) {</td>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="c">    <span class="n" style="color: #333;">pfasta_file</span> <span class="n" style="color: #333;">pf</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pfasta_parse</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pf</span><span class="p">,</span> <span class="n" style="color: #333;">file_descriptor</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="c">            <span class="n" style="color: #333;"><span class="idiff left right">warn</span>x</span><span class="p">(</span><span class="s" style="color: #d14;">"%s: %s"</span><span class="p">,</span> <span class="n" style="color: #333;">file_name</span><span class="p">,</span> <span class="n" style="color: #333;">pfasta_strerror</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pf</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="c">            <span class="n" style="color: #333;"><span class="idiff left right">soft_err</span>x</span><span class="p">(</span><span class="s" style="color: #d14;">"%s: %s"</span><span class="p">,</span> <span class="n" style="color: #333;">file_name</span><span class="p">,</span> <span class="n" style="color: #333;">pfasta_strerror</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pf</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="c">            <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">fail</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -225,7 +227,7 @@ void read_fasta(const char *file_name, dsa_t *dsa) {</td>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c">    <span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC228" class="line" lang="c">            <span class="n" style="color: #333;"><span class="idiff left right">warn</span>x</span><span class="p">(</span><span class="s" style="color: #d14;">"%s: %s"</span><span class="p">,</span> <span class="n" style="color: #333;">file_name</span><span class="p">,</span> <span class="n" style="color: #333;">pfasta_strerror</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pf</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="c">            <span class="n" style="color: #333;"><span class="idiff left right">soft_err</span>x</span><span class="p">(</span><span class="s" style="color: #d14;">"%s: %s"</span><span class="p">,</span> <span class="n" style="color: #333;">file_name</span><span class="p">,</span> <span class="n" style="color: #333;">pfasta_strerror</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pf</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="c">            <span class="n" style="color: #333;">pfasta_seq_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ps</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="c"></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -276,23 +278,30 @@ void print_distances(const struct model *D, const seq_t *sequences, size_t n,</td>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="c">                    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DD</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">estimate</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">datum</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_coverage</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">datum</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">001</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="c">                            <span class="n" style="color: #333;">use_scientific</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="c">                    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">dist</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">warnings</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="c">                            <span class="n" style="color: #333;">EXIT_CODE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="c">                            <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">str</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="c">                                    <span class="s" style="color: #d14;">"For the two sequences '%s' and '%s' the distance "</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="c">                                    <span class="s" style="color: #d14;">"computation failed and is reported as nan. "</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="c">                                    <span class="s" style="color: #d14;">"Please refer to the documentation for further details."</span><span class="p">};</span></span>

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="c">                            <span class="n" style="color: #333;">warnx</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="c">                    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">001</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="c">                            <span class="n" style="color: #333;">use_scientific</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="c">                    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">05</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">warnings</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="c">                            <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">str</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="c">                                    <span class="s" style="color: #d14;">"For the two sequences '%s' and '%s' less than 5%% "</span></span>

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="c">                                    <span class="s" style="color: #d14;">"homology were found (%f and %f, respectively)."</span><span class="p">};</span></span>

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="c">                            <span class="n" style="color: #333;">warnx</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="c">                                      <span class="n" style="color: #333;">model_coverage</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">D</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">)),</span> <span class="n" style="color: #333;">model_coverage</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">D</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">)));</span></span>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="c">                            <span class="n" style="color: #333;">soft_errx</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="c">                    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">dist</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">warnings</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="c">                            <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">coverage1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_coverage</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">D</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="c">                            <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">coverage2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_coverage</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">D</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">coverage1</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">05</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">coverage2</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">05</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="c">                                    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">str</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="c">                                            <span class="s" style="color: #d14;">"For the two sequences '%s' and '%s' less than 5%% "</span></span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="c">                                            <span class="s" style="color: #d14;">"homology were found (%f and %f, respectively)."</span><span class="p">};</span></span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="c">                                    <span class="n" style="color: #333;">soft_errx</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="c">                                                      <span class="n" style="color: #333;">coverage1</span><span class="p">,</span> <span class="n" style="color: #333;">coverage2</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="c">                            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="c">                    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="c">            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="c">    <span class="p">}</span></span>

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</li>

<li id="93f5f7039d98b42c276a3759cba8ff5bea5a2d7e">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#93f5f7039d98b42c276a3759cba8ff5bea5a2d7e"><strong>src/model.c</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -202,6 +202,26 @@ void model_count_equal(model *MM, const char *S, size_t len) {</td>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="c">    <span class="n" style="color: #333;">MM</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">TtoT</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">local_counts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** @brief Convert a nucleotide to a 2bit representation.</span></span>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * We want to map characters:</span></span>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *  A → 0</span></span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *  C → 1</span></span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *  G → 2</span></span>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *  T → 3</span></span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * The trick used below is that the three lower bits of the</span></span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * characters are unique. Thus, they can be used to compute the mapping</span></span>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * above. The mapping itself is done via tricky bitwise operations.</span></span>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param c - input nucleotide</span></span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @returns 2bit representation.</span></span>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="nf" style="color: #900; font-weight: 600;">nucl2bit</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="c">    <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">&=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="c">    <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">^=</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @brief Count the substitutions and add them to the mutation matrix.</span></span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -213,7 +233,7 @@ void model_count_equal(model *MM, const char *S, size_t len) {</td>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">model_count</span><span class="p">(</span><span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">S</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Q</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">len</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">local_counts</span><span class="p">[</span><span class="n" style="color: #333;">MUTCOUNTS</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(<span class="idiff left">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">len</span></span><span class="o" style="font-weight: 600;"><span class="idiff">--</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">S</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Q</span></span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">len</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">S</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Q</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">i</span></span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">S</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Q</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="c"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -222,24 +242,9 @@ void model_count(model *MM, const char *S, const char *Q, size_t len) {</td>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c">                    <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="c">            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/* We want to map characters:</span></span>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 *  A → 0</span></span>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 *  C → 1</span></span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 *  G → 2</span></span>

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 *  T → 3</span></span>

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 * The trick used below is that the three lower bits of the</span></span>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 * characters are unique. Thus, they can be used to compute the mapping</span></span>

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 * above. The mapping itself is done via tricky bitwise operations.</span></span>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 */</span></span>

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nibble_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">7</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nibble_q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">7</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="c">            <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0x20031000</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// Pick the correct two bits representing s and q.</span></span>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">foo</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">mm1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nibble_s</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mh" style="color: #099;"><span class="idiff right">0x3</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">baz</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">mm1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nibble_q</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mh" style="color: #099;"><span class="idiff right">0x3</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">foo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">nucl2bit</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">s</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">baz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">nucl2bit</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">q</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c">            <span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                 * The mutation matrix is symmetric. For convenience we define the</span></span>

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<li id="6647cd41afbb7c523f68ba302195e484f7ac5b4a">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#6647cd41afbb7c523f68ba302195e484f7ac5b4a"><strong>src/process.c</strong></a>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <omp.h></span></span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">shu<span class="idiff left right">prop</span></span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">l</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">shu<span class="idiff left right">string_cum_prob</span></span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">l</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">calculate_bootstrap</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">seq_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sequences</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c">                                             <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,18 +31,17 @@ int calculate_bootstrap(const struct model *M, const seq_t *sequences,</td>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Given some parameters calculate the minimum length for anchors according</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * to the distribution from Haubold et al. (2009).</span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param p - The probability with which an anchor is allowed to be random.</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param p - The probability with which an anchor will be created under a</span></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * random model.</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param g - The the relative amount of GC in the subject.</span></span>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param l - The length of the subject.</span></span>

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<td class="diff-line-num new old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param l - The length of the subject<span class="idiff left right"> (includes revcomp)</span>.</span></span>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @returns The minimum length of an anchor.</span></span>

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="nf" style="color: #900; font-weight: 600;">min_anchor_length</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"></span>

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<td class="diff-line-num new_line old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">prop</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c">     <span class="c1" style="color: #998; font-style: italic;">// Find smallest x with P(X > x) < p</span></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c">     <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span> <span class="n" style="color: #333;">prop</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p</span><span class="p">;</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c">             <span class="n" style="color: #333;">prop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shuprop</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c">     <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">shustring_cum_prob</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c">             <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c">     <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c">     <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -82,18 +81,20 @@ size_t binomial_coefficient(size_t n, size_t k) {</td>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @brief Given `x` this function calculates the probability of a shustring</span></span>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * with a length less than `x`.</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * with a length less or equal to `x` under a random model. This means, it is</span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * the cumulative probability.</span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Let X be the longest shortest unique substring (shustring) at any position.</span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Then this function computes P{X <= x} with respect to the given parameter</span></span>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * set. See Haubold et al. (2009).</span></span>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * set. See Haubold et al. (2009). Note that `x` includes the final mismatch.</span></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Thus, `x` is `match length + 1`.</span></span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param x - The maximum length of a shustring.</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param p - The half of the relative amount of GC in the DNA.</span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param l - The length of the subject.</span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @returns The probability of a certain shustring length.</span></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">shu<span class="idiff left right">prop</span></span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">shu<span class="idiff left right">string_cum_prob</span></span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">x</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ll</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">l</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">k</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,6 +116,106 @@ double shuprop(size_t x, double p, size_t l) {</td>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">_Bool</span> <span class="n" style="color: #333;">bool</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define false 0</span></span>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define true !false</span></span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @brief This structure captures properties of an anchor.</span></span>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">anchor</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/** The position on the subject. */</span></span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">pos_S</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/** The position on the query. */</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">pos_Q</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/** The length of the exact match. */</span></span>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

132

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

133

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC133" class="line" lang="c"><span class="p">};</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

134

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC134" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

135

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

136

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @brief This is a structure of assorted variables needed for anchor finding.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

137

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

138

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC138" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">context</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

139

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC139" class="line" lang="c">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">esa_s</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">C</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

140

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC140" class="line" lang="c">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">query</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

141

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC141" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">query_length</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

142

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC142" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">threshold</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

143

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"><span class="p">};</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

144

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

145

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

146

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @brief Compute the length of the longest common prefix of two strings.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

147

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

148

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param S - One string.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

149

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param Q - Another string.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

150

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param remaining - The length of one of the strings.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

151

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @returns the length of the lcp.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="nf" style="color: #900; font-weight: 600;">lcp</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">S</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Q</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">remaining</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

155

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">remaining</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">S</span><span class="p">[</span><span class="n" style="color: #333;">length</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Q</span><span class="p">[</span><span class="n" style="color: #333;">length</span><span class="p">])</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c">            <span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @brief Check whether the last anchor can be extended by a lucky anchor.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Anchors are defined to be unique and of a minimum length. The uniqueness</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * requires us to search throw the suffix array for a second appearance of the</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * anchor. However, if a left anchor is already unique, we could be sloppy and</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

167

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * drop the uniqueness criterion for the second anchor. This way we can skip the</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * lookup and just compare characters directly. However, for a lucky anchor the</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * match still has to be longer than the threshold.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

170

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

171

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param ctx - Matching context of various variables.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

172

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param last_match - The last anchor.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

173

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param this_match - Input/Output variable for the current match.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

174

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @returns true iff the current match is a lucky anchor.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

175

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

176

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">lucky_anchor</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

177

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c">                                                            <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">anchor</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">last_match</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

178

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c">                                                            <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">anchor</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">this_match</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

179

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

180

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">advance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos_Q</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">last_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos_Q</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

181

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos_Q</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">last_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos_Q</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">last_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

182

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

183

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">try_pos_S</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos_S</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">advance</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

184

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">try_pos_S</span> <span class="o" style="font-weight: 600;">>=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">threshold</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

185

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="c">            <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

186

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

187

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

188

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="c">    <span class="n" style="color: #333;">this_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos_S</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">try_pos_S</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

189

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="c">    <span class="n" style="color: #333;">this_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="c">            <span class="n" style="color: #333;">lcp</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">this_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos_Q</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">S</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">try_pos_S</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

191

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="c">                    <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">query_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">this_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos_Q</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

192

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

193

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">this_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">threshold</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

194

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

195

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @brief Check for a new anchor.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Given the current context and starting position check if the new match is an</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * anchor. The latter requires uniqueness and a certain minimum length.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param ctx - Matching context of various variables.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param last_match - (unused)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param this_match - Input/Output variable for the current match.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @returns true iff an anchor was found.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">anchor</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">context</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="c">                                              <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">anchor</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">last_match</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="c">                                              <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">anchor</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">this_match</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c">    <span class="n" style="color: #333;">lcp_inter_t</span> <span class="n" style="color: #333;">inter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_match_cached</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">C</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">this_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos_Q</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="c">                                                                             <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">query_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">this_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos_Q</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="c">    <span class="n" style="color: #333;">this_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos_S</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SA</span><span class="p">[</span><span class="n" style="color: #333;">inter</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="c">    <span class="n" style="color: #333;">this_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inter</span><span class="p">.</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">inter</span><span class="p">.</span><span class="n" style="color: #333;">l</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">inter</span><span class="p">.</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">inter</span><span class="p">.</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">this_match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">threshold</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @brief Divergence estimation using the anchor technique.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -135,83 +236,72 @@ model dist_anchor(const esa_s *C, const char *query, size_t query_length,</td>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="c">                              <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">gc</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="c">    <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">model</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{.</span><span class="n" style="color: #333;">seq_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query_length</span><span class="p">,</span> <span class="p">.</span><span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">}};</span></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="c">    <span class="n" style="color: #333;">lcp_inter_t</span> <span class="n" style="color: #333;">inter</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">last_pos_Q</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">last_pos_S</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">last_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// This variable indicates that the last anchor was the right anchor of a</span></span>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// pair.</span></span>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">last_was_right_anchor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="c">    <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">anchor</span> <span class="n" style="color: #333;">this_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">};</span></span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="c">    <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">anchor</span> <span class="n" style="color: #333;">last_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">};</span></span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">last_was_right_anchor</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">this_pos_Q</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">this_pos_S</span><span class="p">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">this_length</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

243

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_anchor_length</span><span class="p">(</span><span class="n" style="color: #333;">ANCHOR_P_VALUE</span><span class="p">,</span> <span class="n" style="color: #333;">gc</span><span class="p">,</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

150

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<td class="diff-line-num new_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

244

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC244" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

151

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<td class="diff-line-num new_line old" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC151" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">num_right_anchors</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

152

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<td class="diff-line-num new_line old" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC152" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

153

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<td class="diff-line-num new_line old" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC153" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_anchor_length</span><span class="p">(</span><span class="n" style="color: #333;">RANDOM_ANCHOR_PROP</span><span class="p">,</span> <span class="n" style="color: #333;">gc</span><span class="p">,</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

245

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="c">    <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">context</span> <span class="n" style="color: #333;">ctx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">C</span><span class="p">,</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">query_length</span><span class="p">,</span> <span class="n" style="color: #333;">threshold</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

154

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<td class="diff-line-num new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

246

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

155

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<td class="diff-line-num new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

247

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC247" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// Iterate over the complete query.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

156

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<td class="diff-line-num new_line old" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC156" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">this_pos_Q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">query_length</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

157

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<td class="diff-line-num new_line old" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC157" class="line" lang="c">            <span class="n" style="color: #333;">inter</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

158

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<td class="diff-line-num new_line old" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC158" class="line" lang="c">                    <span class="n" style="color: #333;">get_match_cached</span><span class="p">(</span><span class="n" style="color: #333;">C</span><span class="p">,</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">this_pos_Q</span><span class="p">,</span> <span class="n" style="color: #333;">query_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">this_pos_Q</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

159

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<td class="diff-line-num new_line old" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC159" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

160

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<td class="diff-line-num new_line old" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC160" class="line" lang="c">            <span class="n" style="color: #333;">this_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inter</span><span class="p">.</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">inter</span><span class="p">.</span><span class="n" style="color: #333;">l</span><span class="p">;</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

248

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC248" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">this_match</span><span class="p">.</span><span class="n" style="color: #333;">pos_Q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">query_length</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

161

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<td class="diff-line-num new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

249

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC249" class="line" lang="c"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

162

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<td class="diff-line-num new_line old" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC162" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">inter</span><span class="p">.</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">inter</span><span class="p">.</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">this_length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">threshold</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// Check for lucky anchors and fall back to normal strategy.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lucky_anchor</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">last_match</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">this_match</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="c">                    <span class="n" style="color: #333;">anchor</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">last_match</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">this_match</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="c">                    <span class="c1" style="color: #998; font-style: italic;">// We have reached a new anchor.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="c">                    <span class="n" style="color: #333;">this_pos_S</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SA</span><span class="p">[</span><span class="n" style="color: #333;">inter</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">end_S</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last_match</span><span class="p">.</span><span class="n" style="color: #333;">pos_S</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_match</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">end_Q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last_match</span><span class="p">.</span><span class="n" style="color: #333;">pos_Q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_match</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c">                    <span class="c1" style="color: #998; font-style: italic;">// Check if this can be a right anchor to the last one.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">this_pos_S</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">last_pos_S</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="c">                            <span class="n" style="color: #333;">this_pos_Q</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">last_pos_Q</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">this_pos_S</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">last_pos_S</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="c">                            <span class="n" style="color: #333;">num_right_anchors</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">this_match</span><span class="p">.</span><span class="n" style="color: #333;">pos_S</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">end_S</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="c">                            <span class="n" style="color: #333;">this_match</span><span class="p">.</span><span class="n" style="color: #333;">pos_Q</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">end_Q</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">this_match</span><span class="p">.</span><span class="n" style="color: #333;">pos_S</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">end_S</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="c">                            <span class="c1" style="color: #998; font-style: italic;">// classify nucleotides in the qanchor</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="c">                            <span class="n" style="color: #333;">model_count_equal</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_pos_Q</span><span class="p">,</span> <span class="n" style="color: #333;">last_length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="c">                            <span class="c1" style="color: #998; font-style: italic;">// classify nucleotides in the left qanchor</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="c">                            <span class="n" style="color: #333;">model_count_equal</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_match</span><span class="p">.</span><span class="n" style="color: #333;">pos_Q</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="c">                                                              <span class="n" style="color: #333;">last_match</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

174

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="c">                            <span class="c1" style="color: #998; font-style: italic;">// Count the SNPs in between.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="c">                            <span class="n" style="color: #333;">model_count</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">S</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_pos_S</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_length</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="c">                                                    <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_pos_Q</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_length</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="c">                                                    <span class="n" style="color: #333;">this_pos_Q</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">last_pos_Q</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">last_length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC178" class="line" lang="c">                            <span class="n" style="color: #333;">last_was_right_anchor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="c">                            <span class="n" style="color: #333;">model_count</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">S</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end_S</span><span class="p">,</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end_Q</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="c">                                                    <span class="n" style="color: #333;">this_match</span><span class="p">.</span><span class="n" style="color: #333;">pos_Q</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">end_Q</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="c">                            <span class="n" style="color: #333;">last_was_right_anchor</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c">                    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">last_was_right_anchor</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c">                                    <span class="c1" style="color: #998; font-style: italic;">// If the last was a right anchor, but with the current one,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="c">                                    <span class="c1" style="color: #998; font-style: italic;">// we cannot extend, then add its length.</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="c">                                    <span class="n" style="color: #333;">model_count_equal</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_pos_Q</span><span class="p">,</span> <span class="n" style="color: #333;">last_length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

184

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<td class="diff-line-num new_line old" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC184" class="line" lang="c">                            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">last_length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="c">                                    <span class="n" style="color: #333;">model_count_equal</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_match</span><span class="p">.</span><span class="n" style="color: #333;">pos_Q</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="c">                                                                      <span class="n" style="color: #333;">last_match</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="c">                            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">last_match</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

185

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<td class="diff-line-num new_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="c">                                    <span class="c1" style="color: #998; font-style: italic;">// The last anchor wasn't neither a left or right anchor.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="c">                                    <span class="c1" style="color: #998; font-style: italic;">// But, it was as long as an anchor pair. So still count it.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC187" class="line" lang="c">                                    <span class="n" style="color: #333;">model_count_equal</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_pos_Q</span><span class="p">,</span> <span class="n" style="color: #333;">last_length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="c">                                    <span class="n" style="color: #333;">model_count_equal</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_match</span><span class="p">.</span><span class="n" style="color: #333;">pos_Q</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="c">                                                                      <span class="n" style="color: #333;">last_match</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC190" class="line" lang="c">                            <span class="n" style="color: #333;">last_was_right_anchor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="c">                            <span class="n" style="color: #333;">last_was_right_anchor</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">false</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

191

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<td class="diff-line-num new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

192

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<td class="diff-line-num new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

284

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC284" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

193

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<td class="diff-line-num new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="c">                    <span class="c1" style="color: #998; font-style: italic;">// Cache values for later</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

194

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<td class="diff-line-num new_line old" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="c">                    <span class="n" style="color: #333;">last_pos_Q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this_pos_Q</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC195" class="line" lang="c">                    <span class="n" style="color: #333;">last_pos_S</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this_pos_S</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

196

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<td class="diff-line-num new_line old" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="c">                    <span class="n" style="color: #333;">last_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this_length</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="c">                    <span class="n" style="color: #333;">last_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this_match</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

197

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<td class="diff-line-num new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

287

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

198

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<td class="diff-line-num new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

288

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

199

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<td class="diff-line-num new_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

289

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// Advance</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

200

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<td class="diff-line-num new_line old" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="c">            <span class="n" style="color: #333;">this_<span class="idiff left">pos_Q</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">this_</span>length</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

290

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="c">            <span class="n" style="color: #333;">this_<span class="idiff left">match</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos_Q</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">this_match</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

201

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<td class="diff-line-num new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

291

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

202

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<td class="diff-line-num new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

292

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC292" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

203

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<td class="diff-line-num new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// Very special case: The sequences are identical</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">last_length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">query_length</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

205

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<td class="diff-line-num new_line old" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC205" class="line" lang="c">            <span class="n" style="color: #333;">model_count</span><span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">ret</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">C</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">S</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">last_pos_S</span></span><span class="p">,</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">query_length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">last_<span class="idiff left">match</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">query_length</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="c">            <span class="n" style="color: #333;">model_count<span class="idiff left">_equal</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">ret</span></span><span class="p">,</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">query_length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

206

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<td class="diff-line-num new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="c">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

207

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<td class="diff-line-num new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

297

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

208

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<td class="diff-line-num new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

298

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC298" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// We might miss a few nucleotides if the last anchor was also a right</span></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// anchor. The logic is the same as a few lines above.</span></span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">last_was_right_anchor</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="c">            <span class="n" style="color: #333;">model_count</span><span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">ret</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">C</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">S</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">last_pos_S</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">query</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">last_pos_Q</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">last_</span>length</span><span class="p">);</span></span>

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<td class="diff-line-num old old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="c">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">last_length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="c">            <span class="n" style="color: #333;">model_count_equal</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_<span class="idiff left">pos_Q</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">last_</span>length</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="c">            <span class="n" style="color: #333;">model_count<span class="idiff left">_equal</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">ret</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">query</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">last_match</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos_Q</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">last_match</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">length</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="c">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">last_<span class="idiff left">match</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="c">            <span class="n" style="color: #333;">model_count_equal</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_<span class="idiff left">match</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos_Q</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">last_match</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">length</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -266,7 +356,7 @@ void calculate_distances(seq_t *sequences, size_t n) {</td>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">BOOTSTRAP</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="c">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calculate_bootstrap</span><span class="p">(</span><span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">)</span> <span class="p">{</span></span>

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269

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<td class="diff-line-num new_line old" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC269" class="line" lang="c">                    <span class="n" style="color: #333;"><span class="idiff left right">warn</span>x</span><span class="p">(</span><span class="s" style="color: #d14;">"Bootstrapping failed."</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

359

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="c">                    <span class="n" style="color: #333;"><span class="idiff left right">soft_err</span>x</span><span class="p">(</span><span class="s" style="color: #d14;">"Bootstrapping failed."</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

270

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360

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

271

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361

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

272

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<td class="diff-line-num new_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

362

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC362" class="line" lang="c"></span>

</pre>

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<br>

</li>

<li id="01a89d148d2434a88bba979e1ef4be45506178a5">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#01a89d148d2434a88bba979e1ef4be45506178a5"><strong>test/Makefile.am</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num old old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="make"><span class="nv" style="color: teal;">check_PROGRAMS</span> <span class="o" style="font-weight: 600;">=</span> test_esa test_seq test_fasta</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="make"><span class="nv" style="color: teal;">dist_noinst_DATA</span> <span class="o" style="font-weight: 600;">=</span> test_extra.sh test_random.sh test_join.sh</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="nv" style="color: teal;">check_PROGRAMS</span> <span class="o" style="font-weight: 600;">=</span> test_esa test_seq test_fasta<span class="idiff left right"> test_process</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="make"><span class="nv" style="color: teal;">dist_noinst_DATA</span> <span class="o" style="font-weight: 600;">=</span> test_extra.sh test_random.sh test_join.sh<span class="idiff left right"> nan.sh low_homo.sh</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">if</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">!BUILD_WITH_LIBDIVSUFSORT</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="nv" style="color: teal;">PSUFSORT</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$(top_builddir)</span>/opt/psufsort/libpsufsort.a</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,12 +7,19 @@ PSUFSORT=$(top_builddir)/opt/psufsort/libpsufsort.a</td>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"><span class="nv" style="color: teal;">DUMMY</span><span class="o" style="font-weight: 600;">=</span>dummy.cxx</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="make"><span class="nv" style="color: teal;">test_seq_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_seq.c <span class="idiff left right">..</span>/src/sequence.c</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="make"><span class="nv" style="color: teal;">test_seq_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_seq.c <span class="nv" style="color: teal;"><span class="idiff left right">$(top_srcdir)</span></span>/src/sequence.c</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="nv" style="color: teal;">test_seq_CPPFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-I</span><span class="nv" style="color: teal;">$(top_srcdir)</span>/src <span class="nt" style="color: navy;">-I</span><span class="nv" style="color: teal;">$(top_srcdir)</span>/opt <span class="nt" style="color: navy;">-DDEBUG</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>gnu99</span>

</pre>

</td>

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12

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="nv" style="color: teal;">test_seq_CFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-Wextra</span> <span class="nv" style="color: teal;">$(GLIB_CFLAGS)</span> <span class="nt" style="color: navy;">-Wno-missing-field-initializers</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="nv" style="color: teal;">test_seq_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(GLIB_LIBS)</span> <span class="nv" style="color: teal;">$(top_builddir)</span>/opt/libcompat.a</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="make"><span class="nv" style="color: teal;">test_esa_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_esa.c ../src/esa.c ../src/sequence.c <span class="nv" style="color: teal;">$(top_srcdir)</span>/src/esa.h</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"><span class="nv" style="color: teal;">test_process_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_process.c <span class="nv" style="color: teal;">$(top_srcdir)</span>/src/esa.c <span class="nv" style="color: teal;">$(top_srcdir)</span>/src/io.c <span class="nv" style="color: teal;">$(top_srcdir)</span>/src/model.c <span class="nv" style="color: teal;">$(top_srcdir)</span>/src/process.c <span class="nv" style="color: teal;">$(top_srcdir)</span>/src/sequence.c <span class="nv" style="color: teal;">$(top_srcdir)</span>/src/global.h</span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"><span class="nv" style="color: teal;">test_process_CPPFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(OPENMP_CFLAGS)</span> <span class="nt" style="color: navy;">-I</span><span class="nv" style="color: teal;">$(top_srcdir)</span>/src <span class="nt" style="color: navy;">-I</span><span class="nv" style="color: teal;">$(top_srcdir)</span>/opt <span class="nt" style="color: navy;">-I</span><span class="nv" style="color: teal;">$(top_srcdir)</span>/libs <span class="nt" style="color: navy;">-DDEBUG</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>gnu99</span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"><span class="nv" style="color: teal;">test_process_CFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(OPENMP_CFLAGS)</span> <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-Wextra</span> <span class="nv" style="color: teal;">$(GLIB_CFLAGS)</span> <span class="nt" style="color: navy;">-Wno-missing-field-initializers</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="make"><span class="nv" style="color: teal;">test_process_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(GLIB_LIBS)</span> <span class="nv" style="color: teal;">$(PSUFSORT)</span> <span class="nv" style="color: teal;">$(top_builddir)</span>/opt/libcompat.a <span class="nv" style="color: teal;">$(top_builddir)</span>/libs/libpfasta.a</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="make"><span class="nv" style="color: teal;">test_process_CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(OPENMP_CXXFLAGS)</span> <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-Wextra</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"><span class="nv" style="color: teal;">nodist_EXTRA_test_process_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(DUMMY)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"><span class="nv" style="color: teal;">test_esa_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> test_esa.c <span class="nv" style="color: teal;">$(top_srcdir)</span>/src/esa.c <span class="nv" style="color: teal;">$(top_srcdir)</span>/src/sequence.c <span class="nv" style="color: teal;">$(top_srcdir)</span>/src/esa.h</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"><span class="nv" style="color: teal;">test_esa_CPPFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(OPENMP_CFLAGS)</span> <span class="nt" style="color: navy;">-I</span><span class="nv" style="color: teal;">$(top_srcdir)</span>/libs <span class="nt" style="color: navy;">-I</span><span class="nv" style="color: teal;">$(top_srcdir)</span>/opt <span class="nt" style="color: navy;">-I</span><span class="nv" style="color: teal;">$(top_srcdir)</span>/src <span class="nt" style="color: navy;">-DDEBUG</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>gnu99</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"><span class="nv" style="color: teal;">test_esa_CFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(OPENMP_CFLAGS)</span> <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-Wextra</span> <span class="nv" style="color: teal;">$(GLIB_CFLAGS)</span> <span class="nt" style="color: navy;">-Wno-missing-field-initializers</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"><span class="nv" style="color: teal;">test_esa_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(GLIB_LIBS)</span> <span class="nv" style="color: teal;">$(PSUFSORT)</span> <span class="nv" style="color: teal;">$(top_builddir)</span>/opt/libcompat.a</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="819e7d39af1d85fdb7ad927da43590676d2e5a2e">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#819e7d39af1d85fdb7ad927da43590676d2e5a2e"><strong>test/low_homo.sh</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash -f</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell">./test/test_fasta <span class="nt" style="color: navy;">-l</span> 100000 <span class="o" style="font-weight: 600;">></span> a.fa</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell">./test/test_fasta <span class="nt" style="color: navy;">-l</span> 100000 <span class="o" style="font-weight: 600;">></span> b.fa</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell">./test/test_fasta <span class="nt" style="color: navy;">-l</span> 100 <span class="o" style="font-weight: 600;">></span> both.fa</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>both.fa a.fa | awk <span class="nt" style="color: navy;">-vRS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'>'</span> <span class="s1" style="color: #d14;">'{if($1 == "S0")print ">"$0 > "S0.fa"}'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>both.fa b.fa | awk <span class="nt" style="color: navy;">-vRS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'>'</span> <span class="s1" style="color: #d14;">'{if($1 == "S1")print ">"$0 > "S1.fa"}'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># this is expected to trigger the low homology warning</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell">./src/andi <span class="nt" style="color: navy;">-j</span> S0.fa S1.fa 2>&1 | <span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'homology'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nv" style="color: teal;">EXIT_VAL</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$?</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> EXIT_VAL <span class="nt" style="color: navy;">-ge</span> 1 <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">     </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Triggering low homology failed"</span> <span class="o" style="font-weight: 600;">></span>&2</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'^>'</span> a.fa b.fa both.fa</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">rm <span class="nt" style="color: navy;">-f</span> a.fa b.fa both.fa S0.fa S1.fa</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exit</span> <span class="nv" style="color: teal;">$EXIT_VAL</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="a6c3dd442629f79bf8c5fd2561ef574096e0b943">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#a6c3dd442629f79bf8c5fd2561ef574096e0b943"><strong>test/nan.sh</strong></a>

<hr>

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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash -f</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell">./test/test_fasta <span class="nt" style="color: navy;">-l</span> 10000 <span class="o" style="font-weight: 600;">></span> a.fa</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell">./test/test_fasta <span class="nt" style="color: navy;">-l</span> 10000 <span class="o" style="font-weight: 600;">></span> b.fa</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># this is expected to trigger the nan warning</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell">./src/andi <span class="nt" style="color: navy;">-j</span> a.fa b.fa 2>&1 | <span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'nan'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nv" style="color: teal;">EXIT_VAL</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$?</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> EXIT_VAL <span class="nt" style="color: navy;">-ge</span> 1 <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">     </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Triggering nan failed"</span> <span class="o" style="font-weight: 600;">></span>&2</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'^>'</span> a.fa b.fa both.fa</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">rm <span class="nt" style="color: navy;">-f</span> a.fa b.fa</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exit</span> <span class="nv" style="color: teal;">$EXIT_VAL</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="4c66163cb3f8754139de01c9a49d0f51241d0226">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#4c66163cb3f8754139de01c9a49d0f51241d0226"><strong>test/test_join.sh</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,11 +16,11 @@ rm p1.fasta p2.fasta p3.fasta;</td>

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16

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16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nv" style="color: teal;">RES</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span>./src/andi <span class="nt" style="color: navy;">-m</span> RAW <span class="nt" style="color: navy;">-t</span> 1 <span class="nt" style="color: navy;">-j</span> S0.fasta S1.fasta |</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"> tail <span class="nt" style="color: navy;">-n</span> 1 |</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"> awk <span class="s1" style="color: #d14;">'{print ($2 - 0.1)}'</span> |</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

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<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"> awk <span class="s1" style="color: #d14;">'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.0<span class="idiff left right">1</span>}'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> awk <span class="s1" style="color: #d14;">'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.0<span class="idiff left right">3</span>}'</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"> <span class="k" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

</td>

<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

</td>

<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">test</span> <span class="nv" style="color: teal;">$RES</span> <span class="nt" style="color: navy;">-ne</span> 1<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

23

</td>

<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">     </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The last test computed a distance deviating more than <span class="idiff left right">on</span>e percent from its intended value."</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">     </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The last test computed a distance deviating more than <span class="idiff left right">thre</span>e percent from its intended value."</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"See S0.fasta and S1.fasta for the used sequences."</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

26

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

26

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,11 +38,11 @@ rm p2.fasta p3.fasta;</td>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="nv" style="color: teal;">RES</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span>./src/andi <span class="nt" style="color: navy;">-m</span> RAW <span class="nt" style="color: navy;">-t1</span> <span class="nt" style="color: navy;">-j</span> S0.fasta S1.fasta |</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell">        tail <span class="nt" style="color: navy;">-n</span> 1 |</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell">        awk <span class="s1" style="color: #d14;">'{print ($2 - 0.1)}'</span> |</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

41

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<td class="diff-line-num new_line old" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC41" class="line" lang="shell">        awk <span class="s1" style="color: #d14;">'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.0<span class="idiff left right">1</span>}'</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell">        awk <span class="s1" style="color: #d14;">'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.0<span class="idiff left right">3</span>}'</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell">        <span class="k" style="font-weight: 600;">)</span></span>

</pre>

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43

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43

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"></span>

</pre>

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44

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"><span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">test</span> <span class="nv" style="color: teal;">$RES</span> <span class="nt" style="color: navy;">-ne</span> 1<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

45

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<td class="diff-line-num new_line old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="shell"><span class="k" style="font-weight: 600;">        </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The last test computed a distance deviating more than <span class="idiff left right">on</span>e percent from its intended value."</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

45

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="k" style="font-weight: 600;">        </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The last test computed a distance deviating more than <span class="idiff left right">thre</span>e percent from its intended value."</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell">        <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"See S0.fasta and S1.fasta for the used sequences."</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

47

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

47

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell">        <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

48

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48

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,11 +62,11 @@ rm p1.fasta p2.fasta p3.fasta;</td>

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62

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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"><span class="nv" style="color: teal;">RES</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span>./src/andi <span class="nt" style="color: navy;">-mRAW</span> <span class="nt" style="color: navy;">-t</span> 1 <span class="nt" style="color: navy;">-j</span> S0.fasta S1.fasta |</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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63

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="shell">        tail <span class="nt" style="color: navy;">-n</span> 1 |</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="shell">        awk <span class="s1" style="color: #d14;">'{print ($2 - 0.1)}'</span> |</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="shell">        awk <span class="s1" style="color: #d14;">'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.0<span class="idiff left right">1</span>}'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell">        awk <span class="s1" style="color: #d14;">'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.0<span class="idiff left right">3</span>}'</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell">        <span class="k" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC67" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

68

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<td class="diff-line-num new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

68

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC68" class="line" lang="shell"><span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">test</span> <span class="nv" style="color: teal;">$RES</span> <span class="nt" style="color: navy;">-ne</span> 1<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

69

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<td class="diff-line-num new_line old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="shell"><span class="k" style="font-weight: 600;">        </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The last test computed a distance deviating more than <span class="idiff left right">on</span>e percent from its intended value."</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

69

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="k" style="font-weight: 600;">        </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The last test computed a distance deviating more than <span class="idiff left right">thre</span>e percent from its intended value."</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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70

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell">        <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"See S0.fasta and S1.fasta for the used sequences."</span></span>

</pre>

</td>

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71

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71

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="shell">        <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span></span>

</pre>

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72

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72

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

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<br>

</li>

<li id="047ffddd3115a4a27235eda8eb9e856096824659">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#047ffddd3115a4a27235eda8eb9e856096824659"><strong>test/test_process.c</strong></a>

<hr>

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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "global.h"</span></span>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "process.h"</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <glib.h></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>

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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"></span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">FLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">THREADS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">BOOTSTRAP</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ANCHOR_P_VALUE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">025</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><span class="n" style="color: #333;">gsl_rng</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">RNG</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M_JC</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">shustring_cum_prob</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">l</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">min_anchor_length</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">l</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">test_shustring_cum_prob</span><span class="p">()</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100000</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">gc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">025</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_anchor_length</span><span class="p">(</span><span class="n" style="color: #333;">p_value</span><span class="p">,</span> <span class="n" style="color: #333;">gc</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c">     <span class="n" style="color: #333;">g_assert_cmpfloat</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p_value</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><</span><span class="p">,</span> <span class="n" style="color: #333;">shustring_cum_prob</span><span class="p">(</span><span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">gc</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c">     <span class="n" style="color: #333;">g_assert_cmpfloat</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p_value</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><=</span><span class="p">,</span> <span class="n" style="color: #333;">shustring_cum_prob</span><span class="p">(</span><span class="n" style="color: #333;">threshold</span><span class="p">,</span> <span class="n" style="color: #333;">gc</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c">     <span class="n" style="color: #333;">g_assert_cmpfloat</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p_value</span><span class="p">,</span> <span class="o" style="font-weight: 600;">></span><span class="p">,</span> <span class="n" style="color: #333;">shustring_cum_prob</span><span class="p">(</span><span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">gc</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c">     <span class="n" style="color: #333;">g_test_init</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c">     <span class="n" style="color: #333;">g_test_add_func</span><span class="p">(</span><span class="s" style="color: #d14;">"/process/shustring_cum_prob"</span><span class="p">,</span> <span class="n" style="color: #333;">test_shustring_cum_prob</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c">     <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">g_test_run</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="c1ae1894c1ffe40463c0bf3450a17d5e639a24f3">

<a href="https://salsa.debian.org/med-team/andi/compare/f8aef5c4864e52df519e7e356e88cd9b636584e3...1012cec549f8d12d7510385019949b78c3829938#c1ae1894c1ffe40463c0bf3450a17d5e639a24f3"><strong>test/test_random.sh</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,9 +35,9 @@ do</td>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell">                 ./src/andi <span class="nt" style="color: navy;">-t</span> 1 |</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell">                 tail <span class="nt" style="color: navy;">-n</span> 1 |</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell">                 awk <span class="nt" style="color: navy;">-v</span> <span class="nv" style="color: teal;">dist</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$dist</span> <span class="s1" style="color: #d14;">'{print $2, dist}'</span> |</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

38

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<td class="diff-line-num new_line old" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="shell">                 awk <span class="s1" style="color: #d14;">'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) <= 0.0<span class="idiff left right">2 && abs($1-$2) <= 0.02</span> * $2}'</span><span class="k" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell">                 awk <span class="s1" style="color: #d14;">'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) <= 0.0<span class="idiff left right">55 && abs($1-$2) <= 0.055</span> * $2}'</span><span class="k" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell">         <span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">test</span> <span class="nv" style="color: teal;">$res</span> <span class="nt" style="color: navy;">-ne</span> 1<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

40

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<td class="diff-line-num new_line old" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell"><span class="k" style="font-weight: 600;">                     </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The last test computed a distance deviating more than <span class="idiff left right">two</span> percent from its intended value."</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="k" style="font-weight: 600;">                     </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The last test computed a distance deviating more than <span class="idiff left right">five</span> percent from its intended value."</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell">                 <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"See test_random.fasta for the used sequences."</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell">                 <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"./test/test_fasta -s </span><span class="nv" style="color: teal;">$SEED</span><span class="s2" style="color: #d14;"> -l </span><span class="nv" style="color: teal;">$LENGTH</span><span class="s2" style="color: #d14;"> -d </span><span class="nv" style="color: teal;">$dist</span><span class="s2" style="color: #d14;">"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell">                 head <span class="nt" style="color: navy;">-n</span> 1 ./test/test_random.fasta</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,9 +57,9 @@ do</td>

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<td class="diff-line-num old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell">                 ./src/andi <span class="nt" style="color: navy;">-m</span> RAW <span class="nt" style="color: navy;">-t</span> 1 |</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell">                 tail <span class="nt" style="color: navy;">-n</span> 1 |</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="shell">                 awk <span class="nt" style="color: navy;">-v</span> <span class="nv" style="color: teal;">dist</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$dist</span> <span class="s1" style="color: #d14;">'{print $2, dist}'</span> |</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="shell">                 awk <span class="s1" style="color: #d14;">'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) <= 0.0<span class="idiff left right">2 && abs($1-$2) <= 0.02</span> * $2}'</span><span class="k" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

60

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell">                 awk <span class="s1" style="color: #d14;">'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) <= 0.0<span class="idiff left right">55 && abs($1-$2) <= 0.055</span> * $2}'</span><span class="k" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

61

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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

61

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="shell">         <span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">test</span> <span class="nv" style="color: teal;">$res</span> <span class="nt" style="color: navy;">-ne</span> 1<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

62

</td>

<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="shell"><span class="k" style="font-weight: 600;">                     </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The last test computed a distance deviating more than <span class="idiff left right">two</span> percent from its intended value."</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

62

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="k" style="font-weight: 600;">                     </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The last test computed a distance deviating more than <span class="idiff left right">five</span> percent from its intended value."</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<td class="diff-line-num new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="shell">                 <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"See test_random.fasta for the used sequences."</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

64

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<td class="diff-line-num new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

64

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="shell">                 <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"./test/test_fasta -r -s </span><span class="nv" style="color: teal;">$SEED</span><span class="s2" style="color: #d14;"> -l </span><span class="nv" style="color: teal;">$LENGTH</span><span class="s2" style="color: #d14;"> -d </span><span class="nv" style="color: teal;">$dist</span><span class="s2" style="color: #d14;">"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="shell">                 head <span class="nt" style="color: navy;">-n</span> 1 ./test/test_random.fasta</span>

</pre>

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