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GitLab

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<h3>

Sascha Steinbiss pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/fastaq/commit/e4dd7b7f6d4f01fc0b193e609338be560d7e3bb8">e4dd7b7f</a></strong>

<div>

<span>by Sascha Steinbiss</span>

<i>at 2018-02-22T10:22:16+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.17.0</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/fastaq/commit/2c37df60b20b459c295a2c7fb0a1494e1c1e1ef4">2c37df60</a></strong>

<div>

<span>by Sascha Steinbiss</span>

<i>at 2018-02-22T10:22:17+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.17.0'

Update to upstream version '3.17.0'

with Debian dir bd7c682b84a2f56d5b370c5d0512ad6d156cead9</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/fastaq/commit/28fd27b631f902a53156bc0a181f0d67d5728646">28fd27b6</a></strong>

<div>

<span>by Sascha Steinbiss</span>

<i>at 2018-02-22T10:30:57+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new upstream release

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/fastaq/commit/86c0d168e6d74a7258b4366a305a9987ecc26bd6">86c0d168</a></strong>

<div>

<span>by Sascha Steinbiss</span>

<i>at 2018-02-22T10:31:28+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use secure format link in d/copyright

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/fastaq/commit/4f4862b580cda04998ea00b7b1e66f179e8f8fc6">4f4862b5</a></strong>

<div>

<span>by Sascha Steinbiss</span>

<i>at 2018-02-22T10:55:58+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bump Standards-Version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/fastaq/commit/05de5782f603d1567eef43baa493320625fcc26e">05de5782</a></strong>

<div>

<span>by Sascha Steinbiss</span>

<i>at 2018-02-22T10:56:29+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove patches that aren't applied anyway

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/fastaq/commit/6fdcce8fea8a68d9b85702790b9de62b359a0e22">6fdcce8f</a></strong>

<div>

<span>by Sascha Steinbiss</span>

<i>at 2018-02-22T11:05:40+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use dh11

</pre>

</li>

</ul>

<h4>10 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

debian/compat

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">

debian/copyright

</a>

</li>

<li class="file-stats">

<a href="#1efcfe73a0a10acd9d064ee1030fe2203c6f158f">

<span class="deleted-file">

−

debian/patches/delay-import-statements-for-manpage-creation.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<span class="deleted-file">

−

debian/patches/series

</span>

</a>

</li>

<li class="file-stats">

<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">

<span class="deleted-file">

−

debian/patches/spelling

</span>

</a>

</li>

<li class="file-stats">

<a href="#48d2f0efc4b0d484ae7dbc868d3f14512cbce66d">

pyfastaq/sequences.py

</a>

</li>

<li class="file-stats">

<a href="#856672c263ad1692eb41d8e00952446439a87b46">

pyfastaq/tests/sequences_test.py

</a>

</li>

<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/fastaq/compare/ccbb92dfb5122196c131da85bdd6020a7fd3b6a5...6fdcce8fea8a68d9b85702790b9de62b359a0e22#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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<td class="diff-line-num new old_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">

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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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<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="plaintext">fastaq (3.17.0-1) unstable; urgency=medium</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="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">

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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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<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="plaintext"></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="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">

</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

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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="LC3" class="line" lang="plaintext">  * New upstream release.</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="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">

</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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<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="plaintext">  * Use secure format link in d/copyright.</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="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">

</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

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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="plaintext">  * Bump Standards-Version.</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_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">

</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="plaintext">  * Drop unneeded patches.</span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</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="plaintext">  * Use debhelper 11.</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_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">

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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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<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="plaintext"></span>

</pre>

</td>

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

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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="plaintext"> -- Sascha Steinbiss <satta@debian.org>  Thu, 22 Feb 2018 10:22:55 +0100</span>

</pre>

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</tr>

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

<td class="diff-line-num new old_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">

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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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<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="plaintext"></span>

</pre>

</td>

</tr>

<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="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="plaintext">fastaq (3.16.0-1) unstable; urgency=medium</span>

</pre>

</td>

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<td class="diff-line-num old_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

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

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

</pre>

</td>

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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="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

</td>

<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="plaintext">  [ Steffen Moeller ]</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<a href="https://salsa.debian.org/med-team/fastaq/compare/ccbb92dfb5122196c131da85bdd6020a7fd3b6a5...6fdcce8fea8a68d9b85702790b9de62b359a0e22#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>

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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="plaintext"><span class="idiff left right">9</span></span></pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">11</span></span></pre>

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</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/fastaq/compare/ccbb92dfb5122196c131da85bdd6020a7fd3b6a5...6fdcce8fea8a68d9b85702790b9de62b359a0e22#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ Uploaders: Andreas Tille <tille@debian.org>,</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="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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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">           Sascha Steinbiss <satta@debian.org></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">

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>

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<td class="diff-line-num old old_line" data-linenumber="8" 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">

8

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<td class="diff-line-num new_line old" data-linenumber="8" 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="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= <span class="idiff left right">9</span>),</span>

</pre>

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<td class="diff-line-num new old_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">

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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="plaintext">Build-Depends: debhelper (>= <span class="idiff left right">11</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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">               dh-python,</span>

</pre>

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<td class="diff-line-num old_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">

10

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<td class="diff-line-num 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">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">               python3,</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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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">               python3-setuptools,</span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,7 +14,7 @@ Build-Depends: debhelper (>= 9),</td>

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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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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">               samtools,</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">

15

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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">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">               help2man</span>

</pre>

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<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="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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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">X-Python3-Version: >= 3.2</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">

17

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<td class="diff-line-num new_line old" 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">Standards-Version: 4.1.<span class="idiff left right">1</span></span>

</pre>

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<td class="diff-line-num new old_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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<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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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">3</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="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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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/fastaq.git</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">

19

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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="plaintext">Vcs-Git: https://anonscm.debian.org/git/debian-med/fastaq.git</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="plaintext">Homepage: https://github.com/sanger-pathogens/Fastaq</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<a href="https://salsa.debian.org/med-team/fastaq/compare/ccbb92dfb5122196c131da85bdd6020a7fd3b6a5...6fdcce8fea8a68d9b85702790b9de62b359a0e22#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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

</td>

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>

</pre>

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<td class="diff-line-num new old_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">

</td>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>

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

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: https://github.com/sanger-pathogens/Fastaq</span>

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

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<br>

</li>

<li id="1efcfe73a0a10acd9d064ee1030fe2203c6f158f">

<a href="https://salsa.debian.org/med-team/fastaq/compare/ccbb92dfb5122196c131da85bdd6020a7fd3b6a5...6fdcce8fea8a68d9b85702790b9de62b359a0e22#1efcfe73a0a10acd9d064ee1030fe2203c6f158f"><strong>debian/patches/delay-import-statements-for-manpage-creation.patch</strong>

deleted

</a>

<hr>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: Delay import of Fastaq modules by the python executables </span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> Man pages for this package are being automatically created with through the</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> help2man wrapper called usage_to_man. help2man calls the python executables</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> with the -h option and converts the usage into a man page.</span>

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

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> The first step done by all the executables is the import of the modules deployed</span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> by this package. Since the package is not installed in the system at build time,</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> the man pages would never be properly created.</span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> .</span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> This patch solves this problem by importing the modules in this package after</span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> the argument parsing code.</span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> .</span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> Upstream prefered to keep the code as it is for styling reasons, which is</span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> perfectly reasonable  </span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> .</span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> fastaq (1.5.0-1) UNRELEASED; urgency=low</span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> .</span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff">   * Initial release (Closes: #766321)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff">Author: Jorge Soares <j.s.soares@gmail.com></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_capillary_to_pairs</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_capillary_to_pairs</span></span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_capillary_to_pairs</span></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> import argparse</span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff">     description = 'Given a fasta/q file of capillary reads, makes an interleaved file of read pairs (where more than read from same ligation, takes the longest read) and a file of unpaired reads. Replaces the .p1k/.q1k part of read names to denote fwd/rev reads with /1 and /2',</span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(</span></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> parser.add_argument('infile', help='Name of input fasta/q file')</span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> parser.add_argument('outprefix', help='Prefix of output files', metavar='outfiles prefix')</span>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> options = parser.parse_args()</span>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> tasks.capillary_to_pairs(options.infile, options.outprefix)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_chunker</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_chunker</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_chunker</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> import argparse</span>

</pre>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff">     description = 'Splits a multi fasta/q file into separate files. Splits sequences into chunks of a fixed size. Aims for chunk_size chunks in each file, but allows a little extra, so chunk can be up to (chunk_size + tolerance), to prevent tiny chunks made from the ends of sequences',</span>

</pre>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12,6 +11,10 @@ parser.add_argument('chunk_size', type=i</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> parser.add_argument('tolerance', type=int, help='Tolerance allowed in chunk size')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"> parser.add_argument('--skip_all_Ns', action='store_true', help='Do not output any sequence that consists of all Ns')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"> tasks.split_by_fixed_size(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff">     options.infile,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff">     options.outprefix,</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">

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_count_sequences</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_count_sequences</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_count_sequences</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,11 +1,14 @@</span></span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"> import argparse</span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff">     description = 'Counts the number of sequences in a fasta/q file',</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="76" 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="LC76" class="line" lang="diff">     usage = '%(prog)s <fasta/q in>')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"> parser.add_argument('infile', help='Name of input fasta/q file')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="81" 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">

81

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="82" 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">

82

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="83" 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">

83

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"> print(tasks.count_sequences(options.infile))</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="84" 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">

84

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_deinterleave</span></span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="86" 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="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_deinterleave</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_deinterleave</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" 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="LC88" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="91" 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="LC91" class="line" lang="diff"> import argparse</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="92" 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="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="93" 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="LC93" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="94" 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="LC94" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="95" 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="LC95" class="line" lang="diff">     description = 'Deinterleaves fasta/q file, so that reads are written alternately between two output files',</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" 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="LC96" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -11,4 +10,8 @@ parser.add_argument('infile', help='Name</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"> parser.add_argument('out_fwd', help='Name of output fasta/q file of forwards reads')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" 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="LC98" class="line" lang="diff"> parser.add_argument('out_rev', help='Name of output fasta/q file of reverse reads')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="102" 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">

102

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="103" 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="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="104" 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="LC104" class="line" lang="diff"> tasks.deinterleave(options.infile, options.out_fwd, options.out_rev, fasta_out=options.fasta_out)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="105" 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">

105

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_enumerate_names</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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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="107" 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="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_enumerate_names</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" 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="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_enumerate_names</span></span>

</pre>

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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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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="111" 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">

111

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC111" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="112" 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="0" 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="LC112" class="line" lang="diff"> import argparse</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="113" 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="0" 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="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="114" 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">

114

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC114" class="line" lang="diff"> </span>

</pre>

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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">

115

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="116" 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="0" 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="LC116" class="line" lang="diff">     description = 'Renames sequences in a file, calling them 1,2,3... etc',</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="117" 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="LC117" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12,6 +11,10 @@ parser.add_argument('--keep_suffix', act</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="118" 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="LC118" class="line" lang="diff"> parser.add_argument('infile', help='Name of fasta/q file to be read')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="119" 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="LC119" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output fasta/q file')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="120" 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="LC120" class="line" lang="diff"> options = parser.parse_args()</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">

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"> tasks.enumerate_names(options.infile,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff">                       options.outfile,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff">                       start_index=options.start_index,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_expand_nucleotides</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_expand_nucleotides</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_expand_nucleotides</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"> #!/usr/bin/env python3</span>

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

</pre>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"> import argparse</span>

</pre>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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137

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="138" 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="LC138" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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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">

139

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff">     description = 'Makes all combinations of sequences in input file by using all possibilities of redundant bases. e.g. ART could be AAT or AGT. Assumes input is nucleotides, not amino acids',</span>

</pre>

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,6 +8,10 @@ parser = argparse.ArgumentParser(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"> parser.add_argument('infile', help='Name of input file. Can be any of FASTA, FASTQ, GFF3, EMBL, GBK, Phylip')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output file')</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="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="146" 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="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="147" 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">

147

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></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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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"> tasks.expand_nucleotides(</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="149" 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">

149

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff">     options.infile,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="150" 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">

150

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff">     options.outfile,</span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_extend_gaps</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">

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</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="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_extend_gaps</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_extend_gaps</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="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</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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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff"> #!/usr/bin/env python3</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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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff"> </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">

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"> import argparse</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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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></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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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"> </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">

161

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"> parser = argparse.ArgumentParser(</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">

162

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<td class="diff-line-num new_line old" data-linenumber="0" 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="diff">     description = 'Extends the length of all gaps (and trims the start/end of sequences) in a fasta/q file. Does this by replacing a set number of bases either side of each gap with Ns. Any sequence that ends up as all Ns is lost',</span>

</pre>

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,4 +9,8 @@ parser.add_argument('--trim_number', typ</span></span>

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"> parser.add_argument('infile', help='Name of input fasta/q file')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output fasta/q file')</span>

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff"> tasks.extend_gaps(options.infile, options.outfile, options.trim_number)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_fasta_to_fastq</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_fasta_to_fastq</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_fasta_to_fastq</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<pre style="margin: 0;">-<span id="LC178" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="179" 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="LC179" class="line" lang="diff"> import argparse</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="180" 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="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="diff">     description = 'Given a fasta and qual file, makes a fastq file',</span>

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<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,4 +9,8 @@ parser.add_argument('fasta', help='Name</span></span>

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<pre style="margin: 0;">-<span id="LC185" class="line" lang="diff"> parser.add_argument('qual', help='Name of input quality scores file', metavar='qual in')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output fastq file', metavar='fastq out')</span>

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<pre style="margin: 0;">-<span id="LC187" class="line" lang="diff"> options = parser.parse_args()</span>

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

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<td class="diff-line-num old old_line" data-linenumber="191" 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="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="192" 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="LC192" class="line" lang="diff"> tasks.fasta_to_fastq(options.fasta, options.qual, options.outfile)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_filter</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">

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_filter</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_filter</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="diff"> import argparse</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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<pre style="margin: 0;">-<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="202" 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="LC202" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC203" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="diff">     description = 'Filters a fasta/q file by sequence length and/or by name matching a regular expression',</span>

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -14,6 +13,10 @@ parser.add_argument('-v', '--invert', ac</span></span>

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="diff"> parser.add_argument('infile', help='Name of fasta/q file to be filtered')</span>

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output fasta/q file')</span>

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="diff"> options = parser.parse_args()</span>

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="diff"> tasks.filter(options.infile,</span>

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="diff">              options.outfile,</span>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="diff">              minlength=options.min_length,</span>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_get_ids</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_get_ids</span></span>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_get_ids</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="diff"> import argparse</span>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="diff">     description = 'Gets IDs from each sequence in a fasta or fastq file',</span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(</span></span>

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="diff"> parser.add_argument('infile', help='Name of input fasta/q file')</span>

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output file')</span>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="diff"> options = parser.parse_args()</span>

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="diff"> tasks.get_ids(options.infile, options.outfile)</span>

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_get_seq_flanking_gaps</span></span>

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_get_seq_flanking_gaps</span></span>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_get_seq_flanking_gaps</span></span>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="diff"> import argparse</span>

</pre>

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

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<pre style="margin: 0;">-<span id="LC248" class="line" lang="diff">     description = 'Gets the sequences either side of gaps in a fasta/q file',</span>

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<pre style="margin: 0;">-<span id="LC249" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -11,4 +10,8 @@ parser.add_argument('--right', type=int,</span></span>

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<pre style="margin: 0;">-<span id="LC250" class="line" lang="diff"> parser.add_argument('infile', help='Name of input fasta/q file')</span>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output fasta/q file')</span>

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC253" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="diff"> tasks.get_seqs_flanking_gaps(options.infile, options.outfile, options.left, options.right)</span>

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<pre style="margin: 0;">-<span id="LC258" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_insert_or_delete_bases</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_insert_or_delete_bases</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_insert_or_delete_bases</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC262" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,9 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC263" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<pre style="margin: 0;">-<span id="LC264" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC265" class="line" lang="diff"> import argparse</span>

</pre>

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import sys</span></span>

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import random</span></span>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import sequences, utils, intervals</span></span>

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<pre style="margin: 0;">-<span id="LC269" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

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<pre style="margin: 0;">-<span id="LC271" class="line" lang="diff">     description = 'Deletes or inserts bases at given position(s) from a fasta/q file',</span>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -16,6 +13,11 @@ parser.add_argument('-i','--insert', act</span></span>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="diff"> parser.add_argument('--insert_range', help='Inserts random bases starting after position P in each sequence of the input file. Inserts start + (n-1)*step bases into sequence n.', metavar='P,start,step')</span>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="diff"> options = parser.parse_args()</span>

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import sys</span></span>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import random</span></span>

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import sequences, utils, intervals</span></span>

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC281" class="line" lang="diff"> test_ops = [int(x is not None) for x in [options.delete, options.insert, options.delete_range, options.insert_range]]</span>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="diff"> if sum(test_ops) != 1:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_interleave</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC285" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_interleave</span></span>

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_interleave</span></span>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="diff"> import argparse</span>

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="diff">     description = 'Interleaves two fasta/q files, so that reads are written alternately first/second in output file',</span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,4 +9,8 @@ parser.add_argument('infile_1', help='Na</span></span>

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="diff"> parser.add_argument('infile_2', help='Name of second input fasta/q file')</span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output fasta/q file of interleaved reads')</span>

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<pre style="margin: 0;">-<span id="LC299" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="diff"> tasks.interleave(options.infile_1, options.infile_2, options.outfile)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_long_read_simulate</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_long_read_simulate</span></span>

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_long_read_simulate</span></span>

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="diff"> #!/usr/bin/env python3</span>

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

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<pre style="margin: 0;">-<span id="LC312" class="line" lang="diff"> import argparse</span>

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="diff">     description = 'Simulates long reads from a fasta/q file. Can optionally make insertions into the reads, like pacbio does. If insertions made, coverage calculation is done before the insertions (so total read length may appear longer then expected).',</span>

</pre>

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<pre style="margin: 0;">-<span id="LC317" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -29,8 +28,11 @@ ins_group = parser.add_argument_group('o</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC318" class="line" lang="diff"> ins_group.add_argument('--ins_skip', type=int, help='Insert a random base every --skip bases plus or minus --ins_window. If this option is used, must also use --ins_window.', metavar='INT')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC319" class="line" lang="diff"> ins_group.add_argument('--ins_window', type=int, help='See --ins_skip. If this option is used, must also use --ins_skip.', metavar='INT')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC320" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC322" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC323" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC324" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC325" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC327" class="line" lang="diff"> tasks.make_long_reads(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="diff">     options.infile,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="diff">     options.outfile,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_make_random_contigs</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_make_random_contigs</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC333" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_make_random_contigs</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC335" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC336" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="diff"> import argparse</span>

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<pre style="margin: 0;">-<span id="LC338" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC341" class="line" lang="diff">     description = 'Makes a multi-fasta file of random sequences, all of the same length. Each base has equal chance of being A,C,G or T',</span>

</pre>

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<pre style="margin: 0;">-<span id="LC342" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -14,6 +13,10 @@ parser.add_argument('contigs', type=int,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="diff"> parser.add_argument('length', type=int, help='Length of each contig')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output file')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC345" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC347" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC348" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC349" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="diff"> tasks.make_random_contigs(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="diff">     options.contigs,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC352" class="line" lang="diff">     options.length,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_merge</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC354" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_merge</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC356" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_merge</span></span>

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<pre style="margin: 0;">-<span id="LC357" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC358" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC359" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC360" class="line" lang="diff"> import argparse</span>

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<pre style="margin: 0;">-<span id="LC361" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC362" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC364" class="line" lang="diff">     description = 'Converts multi fasta/q file to single sequence file, preserving original order of sequences',</span>

</pre>

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,6 +9,10 @@ parser.add_argument('infile', help='Name</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC366" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output file')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="diff"> parser.add_argument('-n', '--name', help='Name of sequence in output file [%(default)s]', default='union')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC368" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC369" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC370" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC371" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC372" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="diff"> tasks.merge_to_one_seq(</span>

</pre>

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374

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<pre style="margin: 0;">-<span id="LC374" class="line" lang="diff">     options.infile,</span>

</pre>

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375

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<pre style="margin: 0;">-<span id="LC375" class="line" lang="diff">     options.outfile,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC376" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_replace_bases</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC377" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC378" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_replace_bases</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC379" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_replace_bases</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC380" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC381" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<pre style="margin: 0;">-<span id="LC382" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="diff"> import argparse</span>

</pre>

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<pre style="margin: 0;">-<span id="LC384" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC385" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="386" 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="LC386" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="387" 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">

387

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="diff">     description = 'Replaces all occurences of one letter with another in a fasta/q file',</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="388" 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="LC388" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -11,4 +10,8 @@ parser.add_argument('outfile', help='Nam</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC389" class="line" lang="diff"> parser.add_argument('old', help='Base to be replaced')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="390" 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">

390

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<pre style="margin: 0;">-<span id="LC390" class="line" lang="diff"> parser.add_argument('new', help='Replace with this letter')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC391" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC392" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC393" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="394" 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="LC394" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="395" 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="LC395" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="396" 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="LC396" class="line" lang="diff"> tasks.replace_bases(options.infile, options.outfile, options.old, options.new)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="397" 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="LC397" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_reverse_complement</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="398" 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="LC398" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC399" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_reverse_complement</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC400" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_reverse_complement</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC401" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC402" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<pre style="margin: 0;">-<span id="LC403" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC404" class="line" lang="diff"> import argparse</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="405" 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="LC405" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="406" 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="LC406" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="407" 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="LC407" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="408" 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="LC408" class="line" lang="diff">     description = 'Reverse complements all sequences in a fasta/q file',</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="409" 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="LC409" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC410" class="line" lang="diff"> parser.add_argument('infile', help='Name of input fasta/q file')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="411" 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="LC411" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output fasta/q file')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC412" class="line" lang="diff"> options = parser.parse_args()</span>

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<pre style="margin: 0;">-<span id="LC413" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC414" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC415" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC416" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="diff"> tasks.reverse_complement(options.infile, options.outfile)</span>

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<pre style="margin: 0;">-<span id="LC418" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_scaffolds_to_contigs</span></span>

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<pre style="margin: 0;">-<span id="LC419" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC420" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_scaffolds_to_contigs</span></span>

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<pre style="margin: 0;">-<span id="LC421" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_scaffolds_to_contigs</span></span>

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<pre style="margin: 0;">-<span id="LC422" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC423" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC424" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC425" class="line" lang="diff"> import argparse</span>

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<pre style="margin: 0;">-<span id="LC426" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC427" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC428" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC429" class="line" lang="diff">     description = 'Creates a file of contigs from a file of scaffolds - i.e. breaks at every gap in the input',</span>

</pre>

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<pre style="margin: 0;">-<span id="LC430" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,4 +9,7 @@ parser.add_argument('--number_contigs',</span></span>

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<pre style="margin: 0;">-<span id="LC431" class="line" lang="diff"> parser.add_argument('infile', help='Name of input fasta/q file')</span>

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<pre style="margin: 0;">-<span id="LC432" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output contigs file')</span>

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<pre style="margin: 0;">-<span id="LC433" class="line" lang="diff"> options = parser.parse_args()</span>

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<pre style="margin: 0;">-<span id="LC434" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC435" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC436" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC437" class="line" lang="diff"> tasks.scaffolds_to_contigs(options.infile, options.outfile, number_contigs=options.number_contigs)</span>

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<pre style="margin: 0;">-<span id="LC438" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_search_for_seq</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC439" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC440" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_search_for_seq</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC441" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_search_for_seq</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC442" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC443" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC444" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC445" class="line" lang="diff"> import argparse</span>

</pre>

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<pre style="margin: 0;">-<span id="LC446" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC447" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC448" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC449" class="line" lang="diff">     description = 'Searches for an exact match on a given string and its reverese complement, in every sequences of a fasta/q file. Case insensitive. Guaranteed to find all hits',</span>

</pre>

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<pre style="margin: 0;">-<span id="LC450" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,4 +9,7 @@ parser.add_argument('infile', help='Name</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC451" class="line" lang="diff"> parser.add_argument('outfile', help='Name of outputfile. Tab-delimited output: sequence name, position, strand')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC452" class="line" lang="diff"> parser.add_argument('search_string', help='String to search for in the sequences')</span>

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<pre style="margin: 0;">-<span id="LC453" class="line" lang="diff"> options = parser.parse_args()</span>

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<pre style="margin: 0;">-<span id="LC454" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC455" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC456" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC457" class="line" lang="diff"> tasks.search_for_seq(options.infile, options.outfile, options.search_string)</span>

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<pre style="margin: 0;">-<span id="LC458" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_sequence_trim</span></span>

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<pre style="margin: 0;">-<span id="LC459" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

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<pre style="margin: 0;">-<span id="LC460" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_sequence_trim</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC461" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_sequence_trim</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC462" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC463" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC464" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC465" class="line" lang="diff"> import argparse</span>

</pre>

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<pre style="margin: 0;">-<span id="LC466" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC467" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC468" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC469" class="line" lang="diff">     description = 'Trims sequences off the start of all sequences in a pair of fasta/q files, whenever there is a perfect match. Only keeps a read pair if both reads of the pair are at least a minimum length after any trimming',</span>

</pre>

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<pre style="margin: 0;">-<span id="LC470" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -14,6 +13,10 @@ parser.add_argument('outfile_1', help='N</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC471" class="line" lang="diff"> parser.add_argument('outfile_2', help='Name of output reverse fasta/q file', metavar='out_2')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC472" class="line" lang="diff"> parser.add_argument('trim_seqs', help='Name of fasta/q file of sequences to search for at the start of each input sequence', metavar='trim_seqs')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC473" class="line" lang="diff"> options = parser.parse_args()</span>

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<pre style="margin: 0;">-<span id="LC474" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC475" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC476" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

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477

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<pre style="margin: 0;">-<span id="LC477" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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478

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<pre style="margin: 0;">-<span id="LC478" class="line" lang="diff"> tasks.sequence_trim(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC479" class="line" lang="diff">     options.infile_1,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC480" class="line" lang="diff">     options.infile_2,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC481" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_split_by_base_count</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC482" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC483" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_split_by_base_count</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC484" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_split_by_base_count</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC485" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC486" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC487" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC488" class="line" lang="diff"> import argparse</span>

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<pre style="margin: 0;">-<span id="LC489" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC490" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC491" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="492" 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="LC492" class="line" lang="diff">     description = 'Splits a multi fasta/q file into separate files. Does not split sequences. Puts up to max_bases into each split file. The exception is that any sequence longer than max_bases is put into its own file.',</span>

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493

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<pre style="margin: 0;">-<span id="LC493" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12,4 +11,8 @@ parser.add_argument('max_bases', type=in</span></span>

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494

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<pre style="margin: 0;">-<span id="LC494" class="line" lang="diff"> parser.add_argument('--max_seqs', type=int, help='Max number of sequences in each output split file [no limit]', metavar='INT')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC495" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC496" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC497" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC498" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC499" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC500" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="501" 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="LC501" class="line" lang="diff"> tasks.split_by_base_count(options.infile, options.outprefix, options.max_bases, options.max_seqs)</span>

</pre>

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502

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<pre style="margin: 0;">-<span id="LC502" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_strip_illumina_suffix</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC503" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC504" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_strip_illumina_suffix</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC505" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_strip_illumina_suffix</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC506" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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507

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<pre style="margin: 0;">-<span id="LC507" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="508" 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">

508

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC508" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="509" 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">

509

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC509" class="line" lang="diff"> import argparse</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="510" 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">

510

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<pre style="margin: 0;">-<span id="LC510" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="511" 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">

511

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<pre style="margin: 0;">-<span id="LC511" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="512" 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">

512

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<pre style="margin: 0;">-<span id="LC512" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="513" 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">

513

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC513" class="line" lang="diff">     description = 'Strips /1 or /2 off the end of every read name in a fasta/q file',</span>

</pre>

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514

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<pre style="margin: 0;">-<span id="LC514" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(</span></span>

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<pre style="margin: 0;">-<span id="LC515" class="line" lang="diff"> parser.add_argument('infile', help='Name of input fasta/q file')</span>

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<pre style="margin: 0;">-<span id="LC516" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output fasta/q file')</span>

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<pre style="margin: 0;">-<span id="LC517" class="line" lang="diff"> options = parser.parse_args()</span>

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<pre style="margin: 0;">-<span id="LC518" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC519" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC520" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC521" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC522" class="line" lang="diff"> tasks.strip_illumina_suffix(options.infile, options.outfile)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC523" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_to_fake_qual</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC524" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC525" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_to_fake_qual</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC526" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_to_fake_qual</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC527" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC528" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<pre style="margin: 0;">-<span id="LC529" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC530" class="line" lang="diff"> import argparse</span>

</pre>

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531

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<pre style="margin: 0;">-<span id="LC531" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC532" class="line" lang="diff"> </span>

</pre>

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533

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<pre style="margin: 0;">-<span id="LC533" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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534

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<pre style="margin: 0;">-<span id="LC534" class="line" lang="diff">     description = 'Makes fake quality scores file from a fasta/q file',</span>

</pre>

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<pre style="margin: 0;">-<span id="LC535" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,6 +9,10 @@ parser.add_argument('infile', help='Name</span></span>

</pre>

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536

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<pre style="margin: 0;">-<span id="LC536" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output file')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="537" 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">

537

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<pre style="margin: 0;">-<span id="LC537" class="line" lang="diff"> parser.add_argument('-q', '--qual', type=int, help='Quality score to assign to all bases [%(default)s]', default=40)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="538" 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">

538

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<pre style="margin: 0;">-<span id="LC538" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="539" 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">

539

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<pre style="margin: 0;">-<span id="LC539" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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540

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<pre style="margin: 0;">-<span id="LC540" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="541" 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">

541

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<pre style="margin: 0;">-<span id="LC541" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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542

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<pre style="margin: 0;">-<span id="LC542" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="543" 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">

543

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<pre style="margin: 0;">-<span id="LC543" class="line" lang="diff"> tasks.fastaq_to_fake_qual(</span>

</pre>

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544

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<pre style="margin: 0;">-<span id="LC544" class="line" lang="diff">     options.infile,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="545" 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">

545

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<pre style="margin: 0;">-<span id="LC545" class="line" lang="diff">     options.outfile,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="546" 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">

546

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<pre style="margin: 0;">-<span id="LC546" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_to_fasta</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="547" 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">

547

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<pre style="margin: 0;">-<span id="LC547" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="548" 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">

548

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<pre style="margin: 0;">-<span id="LC548" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_to_fasta</span></span>

</pre>

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549

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<pre style="margin: 0;">-<span id="LC549" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_to_fasta</span></span>

</pre>

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550

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<pre style="margin: 0;">-<span id="LC550" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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551

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC551" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="552" 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">

552

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC552" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="553" 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">

553

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC553" class="line" lang="diff"> import argparse</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="554" 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">

554

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<pre style="margin: 0;">-<span id="LC554" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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555

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<pre style="margin: 0;">-<span id="LC555" class="line" lang="diff"> </span>

</pre>

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556

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<pre style="margin: 0;">-<span id="LC556" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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557

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<pre style="margin: 0;">-<span id="LC557" class="line" lang="diff">     description = 'Converts sequence file to FASTA format',</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="558" 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">

558

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<pre style="margin: 0;">-<span id="LC558" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -11,6 +10,10 @@ parser.add_argument('outfile', help='Nam</span></span>

</pre>

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559

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<pre style="margin: 0;">-<span id="LC559" class="line" lang="diff"> parser.add_argument('-l', '--line_length', type=int, help='Number of bases on each sequence line of output file [%(default)s]', default=60)</span>

</pre>

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560

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<pre style="margin: 0;">-<span id="LC560" class="line" lang="diff"> parser.add_argument('-s', '--strip_after_whitespace', action='store_true', help='Remove everything after first whitesapce in every sequence name')</span>

</pre>

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561

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<pre style="margin: 0;">-<span id="LC561" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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562

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<pre style="margin: 0;">-<span id="LC562" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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563

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<pre style="margin: 0;">-<span id="LC563" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="564" 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">

564

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<pre style="margin: 0;">-<span id="LC564" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="565" 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">

565

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<pre style="margin: 0;">-<span id="LC565" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="566" 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">

566

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<pre style="margin: 0;">-<span id="LC566" class="line" lang="diff"> tasks.to_fasta(</span>

</pre>

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567

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<pre style="margin: 0;">-<span id="LC567" class="line" lang="diff">     options.infile,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="568" 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">

568

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<pre style="margin: 0;">-<span id="LC568" class="line" lang="diff">     options.outfile,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="569" 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">

569

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<pre style="margin: 0;">-<span id="LC569" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_to_mira_xml</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="570" 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">

570

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<pre style="margin: 0;">-<span id="LC570" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="571" 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">

571

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<pre style="margin: 0;">-<span id="LC571" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_to_mira_xml</span></span>

</pre>

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572

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<pre style="margin: 0;">-<span id="LC572" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_to_mira_xml</span></span>

</pre>

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573

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<pre style="margin: 0;">-<span id="LC573" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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574

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<pre style="margin: 0;">-<span id="LC574" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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575

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<pre style="margin: 0;">-<span id="LC575" class="line" lang="diff"> </span>

</pre>

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576

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<pre style="margin: 0;">-<span id="LC576" class="line" lang="diff"> import argparse</span>

</pre>

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<pre style="margin: 0;">-<span id="LC577" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="578" 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="LC578" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="579" 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">

579

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<pre style="margin: 0;">-<span id="LC579" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="580" 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">

580

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<pre style="margin: 0;">-<span id="LC580" class="line" lang="diff">     description = 'Creates an xml file from a fasta/q file of reads, for use with Mira assembler',</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="581" 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">

581

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<pre style="margin: 0;">-<span id="LC581" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(</span></span>

</pre>

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582

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<pre style="margin: 0;">-<span id="LC582" class="line" lang="diff"> parser.add_argument('infile', help='Name of input fasta/q file')</span>

</pre>

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583

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<pre style="margin: 0;">-<span id="LC583" class="line" lang="diff"> parser.add_argument('xml_out', help='Name of output xml file')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="584" 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">

584

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<pre style="margin: 0;">-<span id="LC584" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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585

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<pre style="margin: 0;">-<span id="LC585" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC586" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC587" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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588

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<pre style="margin: 0;">-<span id="LC588" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC589" class="line" lang="diff"> tasks.fastaq_to_mira_xml(options.infile, options.xml_out)</span>

</pre>

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590

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<pre style="margin: 0;">-<span id="LC590" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_to_orfs_gff</span></span>

</pre>

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591

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC591" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC592" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_to_orfs_gff</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC593" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_to_orfs_gff</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC594" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC595" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<pre style="margin: 0;">-<span id="LC596" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC597" class="line" lang="diff"> import argparse</span>

</pre>

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<pre style="margin: 0;">-<span id="LC598" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

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<td class="diff-line-num old old_line" data-linenumber="599" 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">

599

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<pre style="margin: 0;">-<span id="LC599" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="600" 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="LC600" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="601" 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="0" 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="LC601" class="line" lang="diff">     description = 'Writes a GFF file of open reading frames from a fasta/q file',</span>

</pre>

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602

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<pre style="margin: 0;">-<span id="LC602" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,4 +9,8 @@ parser.add_argument('--min_length', type</span></span>

</pre>

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603

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<pre style="margin: 0;">-<span id="LC603" class="line" lang="diff"> parser.add_argument('infile', help='Name of input fasta/q file')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="604" 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">

604

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<pre style="margin: 0;">-<span id="LC604" class="line" lang="diff"> parser.add_argument('gff_out', help='Name of output gff file')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="605" 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">

605

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<pre style="margin: 0;">-<span id="LC605" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC606" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC607" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC608" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="609" 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="LC609" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC610" class="line" lang="diff"> tasks.fastaq_to_orfs_gff(options.infile, options.gff_out, min_length=options.min_length)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC611" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_to_perfect_reads</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="612" 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="0" 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="LC612" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC613" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_to_perfect_reads</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC614" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_to_perfect_reads</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="615" 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="LC615" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,10 +1,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC616" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<pre style="margin: 0;">-<span id="LC617" class="line" lang="diff"> </span>

</pre>

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618

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<pre style="margin: 0;">-<span id="LC618" class="line" lang="diff"> import argparse</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="619" 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">

619

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<pre style="margin: 0;">-<span id="LC619" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import random</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="620" 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">

620

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<pre style="margin: 0;">-<span id="LC620" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from math import floor, ceil</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="621" 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">

621

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<pre style="margin: 0;">-<span id="LC621" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import sequences, utils</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="622" 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">

622

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<pre style="margin: 0;">-<span id="LC622" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import sys</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="623" 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">

623

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<pre style="margin: 0;">-<span id="LC623" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="624" 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">

624

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<pre style="margin: 0;">-<span id="LC624" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="625" 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">

625

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<pre style="margin: 0;">-<span id="LC625" class="line" lang="diff">     description = 'Makes perfect paired end fastq reads from a fasta/q file, with insert sizes sampled from a normal distribution. Read orientation is innies. Output is an interleaved fastq file.',</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="626" 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">

626

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<pre style="margin: 0;">-<span id="LC626" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -20,6 +16,12 @@ parser.add_argument('--no_n', action='st</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="627" 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">

627

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<pre style="margin: 0;">-<span id="LC627" class="line" lang="diff"> parser.add_argument('--seed', type=int, help='Seed for random number generator. Default is to use python\'s default', default=None, metavar='INT')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="628" 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">

628

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<pre style="margin: 0;">-<span id="LC628" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="629" 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">

629

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<pre style="margin: 0;">-<span id="LC629" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="630" 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">

630

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC630" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="631" 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">

631

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<pre style="margin: 0;">-<span id="LC631" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import random</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="632" 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">

632

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<pre style="margin: 0;">-<span id="LC632" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from math import floor, ceil</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="633" 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">

633

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC633" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import sequences, utils</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="634" 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">

634

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC634" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import sys</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="635" 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">

635

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC635" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="636" 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">

636

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC636" class="line" lang="diff"> random.seed(a=options.seed)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="637" 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">

637

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC637" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="638" 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">

638

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC638" class="line" lang="diff"> seq_reader = sequences.file_reader(options.infile)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC639" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_to_random_subset</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC640" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC641" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_to_random_subset</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC642" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_to_random_subset</span></span>

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<pre style="margin: 0;">-<span id="LC643" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,9 +1,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC644" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC645" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC646" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import sys</span></span>

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<pre style="margin: 0;">-<span id="LC647" class="line" lang="diff"> import argparse</span>

</pre>

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<pre style="margin: 0;">-<span id="LC648" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import random</span></span>

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<pre style="margin: 0;">-<span id="LC649" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import sequences, utils</span></span>

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<pre style="margin: 0;">-<span id="LC650" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC651" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC652" class="line" lang="diff">     description = 'Takes a random subset of reads from a fasta/q file and optionally the corresponding read ' +</span>

</pre>

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<pre style="margin: 0;">-<span id="LC653" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -15,6 +12,11 @@ parser.add_argument('outfile', help='Nam</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC654" class="line" lang="diff"> parser.add_argument('probability', type=int, help='Probability of keeping any given read (pair) in [0,100]', metavar='INT')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC655" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC656" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC657" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC658" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import sys</span></span>

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<pre style="margin: 0;">-<span id="LC659" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import random</span></span>

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<pre style="margin: 0;">-<span id="LC660" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import sequences, utils</span></span>

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<pre style="margin: 0;">-<span id="LC661" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC662" class="line" lang="diff"> seq_reader = sequences.file_reader(options.infile)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC663" class="line" lang="diff"> fout = utils.open_file_write(options.outfile)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC664" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC665" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_to_tiling_bam</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC666" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC667" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_to_tiling_bam</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC668" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_to_tiling_bam</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC669" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,9 +1,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC670" class="line" lang="diff"> #!/usr/bin/env python3</span>

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<pre style="margin: 0;">-<span id="LC671" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC672" class="line" lang="diff"> import argparse</span>

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<pre style="margin: 0;">-<span id="LC673" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import sys</span></span>

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<pre style="margin: 0;">-<span id="LC674" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import os</span></span>

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<pre style="margin: 0;">-<span id="LC675" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import sequences, utils</span></span>

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<pre style="margin: 0;">-<span id="LC676" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC677" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC678" class="line" lang="diff">     description = 'Takes a fasta/q file. Makes a BAM file containing perfect (unpaired) reads tiling the whole genome',</span>

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<pre style="margin: 0;">-<span id="LC679" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -17,6 +14,11 @@ parser.add_argument('outfile', help='Nam</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC680" class="line" lang="diff"> parser.add_argument('--read_group', help='Add the given read group ID to all reads [%(default)s]' ,default='42')</span>

</pre>

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681

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</td>

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<pre style="margin: 0;">-<span id="LC681" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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682

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<pre style="margin: 0;">-<span id="LC682" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="683" 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">

683

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC683" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="684" 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">

684

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<pre style="margin: 0;">-<span id="LC684" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import sys</span></span>

</pre>

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685

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<pre style="margin: 0;">-<span id="LC685" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import os</span></span>

</pre>

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686

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<pre style="margin: 0;">-<span id="LC686" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import sequences, utils</span></span>

</pre>

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687

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<pre style="margin: 0;">-<span id="LC687" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="688" 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">

688

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC688" class="line" lang="diff"> # make a header first  - we need to add the @RG line to the default header made by samtools</span>

</pre>

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689

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<pre style="margin: 0;">-<span id="LC689" class="line" lang="diff"> tmp_empty_file = options.outfile + '.tmp.empty'</span>

</pre>

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690

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<pre style="margin: 0;">-<span id="LC690" class="line" lang="diff"> f = utils.open_file_write(tmp_empty_file)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="691" 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">

691

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<pre style="margin: 0;">-<span id="LC691" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_to_unique_by_id</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="692" 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">

692

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC692" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="693" 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">

693

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<pre style="margin: 0;">-<span id="LC693" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_to_unique_by_id</span></span>

</pre>

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694

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<pre style="margin: 0;">-<span id="LC694" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_to_unique_by_id</span></span>

</pre>

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695

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC695" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="696" 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">

696

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC696" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="697" 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">

697

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC697" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="698" 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">

698

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC698" class="line" lang="diff"> import argparse</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="699" 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">

699

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC699" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

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700

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC700" class="line" lang="diff"> </span>

</pre>

</td>

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701

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<pre style="margin: 0;">-<span id="LC701" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="702" 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">

702

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<pre style="margin: 0;">-<span id="LC702" class="line" lang="diff">     description = 'Removes duplicate sequences from a fasta/q file, based on their names. If the same name is found more than once, then the longest sequence is kept. Order of sequences is preserved in output',</span>

</pre>

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703

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<pre style="margin: 0;">-<span id="LC703" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="704" 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">

704

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC704" class="line" lang="diff"> parser.add_argument('infile', help='Name of input fasta/q file')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="705" 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">

705

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC705" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output fasta/q file')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="706" 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">

706

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC706" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="707" 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">

707

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<pre style="margin: 0;">-<span id="LC707" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="708" 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">

708

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC708" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="709" 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">

709

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC709" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="710" 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">

710

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<pre style="margin: 0;">-<span id="LC710" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="711" 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">

711

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC711" class="line" lang="diff"> tasks.to_unique_by_id(options.infile, options.outfile)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="712" 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">

712

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC712" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_translate</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="713" 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">

713

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC713" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="714" 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">

714

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<pre style="margin: 0;">-<span id="LC714" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_translate</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="715" 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">

715

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<td class="diff-line-num new_line old" data-linenumber="0" 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>

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<pre style="margin: 0;">-<span id="LC715" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_translate</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="716" 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">

716

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC716" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="717" 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">

717

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC717" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="718" 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">

718

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC718" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="719" 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">

719

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<td class="diff-line-num new_line old" data-linenumber="0" 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>

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<pre style="margin: 0;">-<span id="LC719" class="line" lang="diff"> import argparse</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="720" 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">

720

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC720" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="721" 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">

721

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC721" class="line" lang="diff"> </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="722" 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">

722

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC722" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="723" 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">

723

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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>

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<pre style="margin: 0;">-<span id="LC723" class="line" lang="diff">     description = 'Translates all sequences in a fasta or fastq file. Output is always fasta format',</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="724" 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">

724

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC724" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,4 +9,8 @@ parser.add_argument('--frame', type=int,</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="725" 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">

725

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC725" class="line" lang="diff"> parser.add_argument('infile', help='Name of fasta/q file to be translated', metavar='in.fasta/q')</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="726" 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">

726

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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>

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<pre style="margin: 0;">-<span id="LC726" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output fasta file', metavar='out.fasta')</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="727" 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">

727

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC727" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="728" 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">

728

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC728" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</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="729" 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">

729

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC729" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</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="730" 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">

730

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC730" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="731" 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">

731

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC731" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</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="732" 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">

732

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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>

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<pre style="margin: 0;">-<span id="LC732" class="line" lang="diff"> tasks.translate(options.infile, options.outfile, frame=options.frame)</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="733" 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">

733

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC733" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_trim_Ns_at_end</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="734" 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">

734

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC734" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</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="735" 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">

735

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC735" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_trim_Ns_at_end</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="736" 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">

736

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC736" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_trim_Ns_at_end</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="737" 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">

737

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC737" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</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="738" 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">

738

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC738" class="line" lang="diff"> #!/usr/bin/env python3</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="739" 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">

739

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC739" class="line" lang="diff"> </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="740" 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">

740

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC740" class="line" lang="diff"> import argparse</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="741" 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">

741

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC741" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

</pre>

</td>

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742

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<pre style="margin: 0;">-<span id="LC742" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="743" 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">

743

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC743" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="744" 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">

744

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<pre style="margin: 0;">-<span id="LC744" class="line" lang="diff">     description = 'Trims any Ns off each sequence in a fasta/q file. Does nothing to gaps in the middle, just trims the ends',</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="745" 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">

745

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<pre style="margin: 0;">-<span id="LC745" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,4 +8,8 @@ parser = argparse.ArgumentParser(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="746" 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">

746

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<pre style="margin: 0;">-<span id="LC746" class="line" lang="diff"> parser.add_argument('infile', help='Name of input fasta/q file')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="747" 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">

747

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<pre style="margin: 0;">-<span id="LC747" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output fasta/q file')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="748" 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">

748

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<pre style="margin: 0;">-<span id="LC748" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="749" 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">

749

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<pre style="margin: 0;">-<span id="LC749" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="750" 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">

750

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<pre style="margin: 0;">-<span id="LC750" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="751" 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">

751

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<pre style="margin: 0;">-<span id="LC751" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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752

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<pre style="margin: 0;">-<span id="LC752" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="753" 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">

753

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<pre style="margin: 0;">-<span id="LC753" class="line" lang="diff"> tasks.trim_Ns_at_end(options.infile, options.outfile)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="754" 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">

754

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<pre style="margin: 0;">-<span id="LC754" class="line" lang="diff"><span class="gh" style="color: #999;">Index: fastaq/scripts/fastaq_trim_ends</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="755" 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">

755

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC755" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="756" 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">

756

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<pre style="margin: 0;">-<span id="LC756" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- fastaq.orig/scripts/fastaq_trim_ends</span></span>

</pre>

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757

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<pre style="margin: 0;">-<span id="LC757" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ fastaq/scripts/fastaq_trim_ends</span></span>

</pre>

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758

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<pre style="margin: 0;">-<span id="LC758" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,6 @@</span></span>

</pre>

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759

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC759" class="line" lang="diff"> #!/usr/bin/env python3</span>

</pre>

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760

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<pre style="margin: 0;">-<span id="LC760" class="line" lang="diff"> </span>

</pre>

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761

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<pre style="margin: 0;">-<span id="LC761" class="line" lang="diff"> import argparse</span>

</pre>

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762

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<pre style="margin: 0;">-<span id="LC762" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from fastaq import tasks</span></span>

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<pre style="margin: 0;">-<span id="LC763" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC764" class="line" lang="diff"> parser = argparse.ArgumentParser(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC765" class="line" lang="diff">     description = 'Trims set number of bases off each sequence in a fasta/q file',</span>

</pre>

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<pre style="margin: 0;">-<span id="LC766" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -11,4 +10,8 @@ parser.add_argument('start_trim', type=i</span></span>

</pre>

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767

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<pre style="margin: 0;">-<span id="LC767" class="line" lang="diff"> parser.add_argument('end_trim', type=int, help='Number of bases to trim off end')</span>

</pre>

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768

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<pre style="margin: 0;">-<span id="LC768" class="line" lang="diff"> parser.add_argument('outfile', help='Name of output fasta/q file')</span>

</pre>

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769

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<pre style="margin: 0;">-<span id="LC769" class="line" lang="diff"> options = parser.parse_args()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC770" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC771" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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772

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<pre style="margin: 0;">-<span id="LC772" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from fastaq import tasks</span></span>

</pre>

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773

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<pre style="margin: 0;">-<span id="LC773" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC774" class="line" lang="diff"> tasks.trim(options.infile, options.outfile, options.start_trim, options.end_trim)</span></pre>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/fastaq/compare/ccbb92dfb5122196c131da85bdd6020a7fd3b6a5...6fdcce8fea8a68d9b85702790b9de62b359a0e22#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong>

deleted

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">#delay-import-statements-for-manpage-creation.patch</span></pre>

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<br>

</li>

<li id="e4c19aed51618bf0c7ebd03189c67e422f84d4eb">

<a href="https://salsa.debian.org/med-team/fastaq/compare/ccbb92dfb5122196c131da85bdd6020a7fd3b6a5...6fdcce8fea8a68d9b85702790b9de62b359a0e22#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Description: spelling </span>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Author: Sascha Steinbiss <satta@debian.org></span>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">--- a/pyfastaq/runners/make_random_contigs.py</span>

</pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">+++ b/pyfastaq/runners/make_random_contigs.py</span>

</pre>

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5

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">@@ -9,7 +9,7 @@</span>

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6

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">     parser.add_argument('--name_by_letters', action='store_true', help='Name the contigs A,B,C,... will start at A again if you get to Z')</span>

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7

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">     parser.add_argument('--prefix', help='Prefix to add to start of every sequence name', default='')</span>

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8

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">     parser.add_argument('--seed', type=int, help='Seed for random number generator. Default is to use python\'s default', default=None)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">-    parser.add_argument('contigs', type=int, help='Nunber of contigs to make')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">+    parser.add_argument('contigs', type=int, help='Number of contigs to make')</span>

</pre>

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11

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">     parser.add_argument('length', type=int, help='Length of each contig')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">     parser.add_argument('outfile', help='Name of output file')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">     options = parser.parse_args()</span></pre>

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<br>

</li>

<li id="48d2f0efc4b0d484ae7dbc868d3f14512cbce66d">

<a href="https://salsa.debian.org/med-team/fastaq/compare/ccbb92dfb5122196c131da85bdd6020a7fd3b6a5...6fdcce8fea8a68d9b85702790b9de62b359a0e22#48d2f0efc4b0d484ae7dbc868d3f14512cbce66d"><strong>pyfastaq/sequences.py</strong></a>

<hr>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">copy</span></span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">string</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">random</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Counter</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfastaq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">utils</span><span class="p">,</span> <span class="n" style="color: #333;">intervals</span><span class="p">,</span> <span class="n" style="color: #333;">genetic_codes</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Error</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">):</span> <span class="k" style="font-weight: 600;">pass</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">@@ -465,6 +464,47 @@ class Fasta:</td>

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python">        <span class="s" style="color: #d14;">'''Returns a Fasta sequence, translated into amino acids. Starts translating from 'frame', where frame expected to be 0,1 or 2'''</span></span>

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">genetic_codes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">codes</span><span class="p">[</span><span class="n" style="color: #333;">genetic_code</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">:</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">(),</span> <span class="s" style="color: #d14;">'X'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">frame</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</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;">frame</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)]))</span></span>

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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">gc_content</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">as_decimal</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns the GC content for the sequence.</span></span>

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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"><span class="s" style="color: #d14;">        Notes:</span></span>

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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"><span class="s" style="color: #d14;">            This method ignores N when calculating the length of the sequence.</span></span>

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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"><span class="s" style="color: #d14;">            It does not, however ignore other ambiguous bases. It also only</span></span>

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"><span class="s" style="color: #d14;">            includes the ambiguous base S (G or C). In this sense the method is</span></span>

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python"><span class="s" style="color: #d14;">            conservative with its calculation.</span></span>

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

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python"><span class="s" style="color: #d14;">        Args:</span></span>

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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"><span class="s" style="color: #d14;">            as_decimal (bool): Return the result as a decimal. Setting to False</span></span>

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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"><span class="s" style="color: #d14;">            will return as a percentage. i.e for the sequence GCAT it will</span></span>

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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python"><span class="s" style="color: #d14;">            return 0.5 by default and 50.00 if set to False.</span></span>

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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"><span class="s" style="color: #d14;">        Returns:</span></span>

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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"><span class="s" style="color: #d14;">            float: GC content calculated as the number of G, C, and S divided</span></span>

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<pre style="margin: 0;">+<span id="LC482" class="line" lang="python"><span class="s" style="color: #d14;">            by the number of (non-N) bases (length).</span></span>

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<pre style="margin: 0;">+<span id="LC483" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC484" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

485

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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python">        <span class="n" style="color: #333;">gc_total</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

486

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<pre style="margin: 0;">+<span id="LC486" class="line" lang="python">        <span class="n" style="color: #333;">num_bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

487

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<pre style="margin: 0;">+<span id="LC487" class="line" lang="python">        <span class="n" style="color: #333;">n_tuple</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="s" style="color: #d14;">'nN'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

488

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<pre style="margin: 0;">+<span id="LC488" class="line" lang="python">        <span class="n" style="color: #333;">accepted_bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="s" style="color: #d14;">'cCgGsS'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

489

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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

490

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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># counter sums all unique characters in sequence. Case insensitive.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

491

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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">count</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Counter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

492

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<pre style="margin: 0;">+<span id="LC492" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

493

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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;"># dont count N in the number of bases</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

494

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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">base</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">n_tuple</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

495

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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python">                <span class="n" style="color: #333;">num_bases</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC496" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC497" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">base</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">accepted_bases</span><span class="p">:</span>  <span class="c" style="color: #998; font-style: italic;"># S is a G or C</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

498

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<pre style="margin: 0;">+<span id="LC498" class="line" lang="python">                    <span class="n" style="color: #333;">gc_total</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

499

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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

500

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python">        <span class="n" style="color: #333;">gc_content</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gc_total</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">num_bases</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

501

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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="LC501" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">as_decimal</span><span class="p">:</span>  <span class="c" style="color: #998; font-style: italic;"># return as percentage</span></span>

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<pre style="margin: 0;">+<span id="LC503" class="line" lang="python">            <span class="n" style="color: #333;">gc_content</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">100</span></span>

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC505" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gc_content</span></span>

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<pre style="margin: 0;">+<span id="LC506" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Embl</span><span class="p">(</span><span class="n" style="color: #333;">Fasta</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python">    <span class="s" style="color: #d14;">'''Exactly the same as Fasta, but reading seqs from a file works differently'''</span></span>

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<br>

</li>

<li id="856672c263ad1692eb41d8e00952446439a87b46">

<a href="https://salsa.debian.org/med-team/fastaq/compare/ccbb92dfb5122196c131da85bdd6020a7fd3b6a5...6fdcce8fea8a68d9b85702790b9de62b359a0e22#856672c263ad1692eb41d8e00952446439a87b46"><strong>pyfastaq/tests/sequences_test.py</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">@@ -520,6 +520,19 @@ class TestFasta(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC520" class="line" lang="python">            <span class="n" style="color: #333;">fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC521" class="line" lang="python">            <span class="n" style="color: #333;">fa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split_capillary_id</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC522" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC523" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_gc_content</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC524" class="line" lang="python">        <span class="s" style="color: #d14;">"""Test GC content calculation works as expected"""</span></span>

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<pre style="margin: 0;">+<span id="LC525" class="line" lang="python">        <span class="n" style="color: #333;">tests</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cgCG'</span><span class="p">),</span> <span class="mf" style="color: #099;">1.0</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC527" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'tTaA'</span><span class="p">),</span> <span class="mf" style="color: #099;">0.0</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC528" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GCAT'</span><span class="p">),</span> <span class="mf" style="color: #099;">0.5</span><span class="p">),</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

529

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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="LC529" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GCATNN'</span><span class="p">),</span> <span class="mf" style="color: #099;">0.5</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="523" style="width: 35px; color: rgba(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="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

530

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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="LC530" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GCATNNS'</span><span class="p">),</span> <span class="mf" style="color: #099;">0.6</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="523" style="width: 35px; color: rgba(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="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

531

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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="LC531" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GCATNNSK'</span><span class="p">),</span> <span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); 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="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

532

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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="LC532" class="line" lang="python">        <span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); 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="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

533

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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="LC533" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">test</span><span class="p">,</span> <span class="n" style="color: #333;">answer</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tests</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="523" style="width: 35px; color: rgba(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="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

534

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gc_content</span><span class="p">(),</span> <span class="n" style="color: #333;">answer</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

535

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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="LC535" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gc_content</span><span class="p">(</span><span class="n" style="color: #333;">as_decimal</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">),</span> <span class="n" style="color: #333;">answer</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span></span>

</pre>

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523

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<td class="diff-line-num new_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

536

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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="LC536" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

524

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537

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<pre style="margin: 0;"> <span id="LC537" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestEmbl</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>

</pre>

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525

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<td class="diff-line-num new_line" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

538

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<pre style="margin: 0;"> <span id="LC538" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_get_id_from_header_line</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/fastaq/compare/ccbb92dfb5122196c131da85bdd6020a7fd3b6a5...6fdcce8fea8a68d9b85702790b9de62b359a0e22#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</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="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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ from setuptools import setup, find_packages</td>

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4

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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="python"></span>

</pre>

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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="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>

</pre>

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6

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

<pre style="margin: 0;"> <span id="LC6" class="line" lang="python">    <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'pyfastaq'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="7" 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">

7

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<td class="diff-line-num new_line old" data-linenumber="7" 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="LC7" class="line" lang="python">    <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'3.1<span class="idiff left right">6</span>.0'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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="python">    <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'3.1<span class="idiff left right">7</span>.0'</span><span class="p">,</span></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="python">    <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Script to manipulate FASTA and FASTQ files, plus API for developers'</span><span class="p">,</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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python">    <span class="n" style="color: #333;">packages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_packages</span><span class="p">(),</span></span>

</pre>

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<td class="diff-line-num old_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">

10

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<td class="diff-line-num 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">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python">    <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Martin Hunt'</span><span class="p">,</span></span>

</pre>

</td>

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