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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/lambda-align">Debian Med / lambda-align</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/lambda-align/commit/142f48e49a0036a7836f9afdd24d666432a6c95e">142f48e4</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2018-02-17T09:30:44-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lambda-align/commit/5ba1150e64b854a11cb86c047dfdd30ad47417d7">5ba1150e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2018-02-17T09:30:48-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.0.3'
Update to upstream version '1.0.3'
with Debian dir f30a179d18680e921a29bd81266cc1b7d842aee3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lambda-align/commit/8975dc195c8293867e464a3dc4e32c42a0ed9c74">8975dc19</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2018-02-17T09:35:51-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">1.0.3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lambda-align/commit/5ab031729a594272dbdab2a056abe88ed24b5ea1">5ab03172</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2018-02-17T11:27:11-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add CWL descriptions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lambda-align/commit/9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83">9c3a2f5c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2018-02-17T12:19:24-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Run the unit tests, also as AutoPkgTests
</pre>
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<h4>12 changed files:</h4>
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<li class="file-stats">
<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
<span class="new-file">
+
debian/README.source
</span>
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</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#782a36ed6745573288114239783779001929336b">
<span class="new-file">
+
debian/cwl/lambda.cwl
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<li class="file-stats">
<a href="#e2a5ec806298fab5b917bf10ca91997dab840655">
<span class="new-file">
+
debian/cwl/lambda_indexer.cwl
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<li class="file-stats">
<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">
<span class="deleted-file">
−
debian/lintian-overrides
</span>
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<li class="file-stats">
<a href="#6f022ae6349b36b113053d3955c70c2276bed7cf">
debian/patches/force-link-rt-pthread.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
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<li class="file-stats">
<a href="#aab2726ed6daf419caf178b1480b6d7da8a85af6">
<span class="new-file">
+
debian/tests/run-tests
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<li class="file-stats">
<a href="#7be417b8ea0a866946b052f8b0de545ebdaf48b3">
src/holders.hpp
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<li class="file-stats">
<a href="#7552499545cad9fe761b98d5142c0e067cda8faf">
src/options.hpp
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</ul>
<h4>Changes:</h4>
<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>
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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">The cwl/ directory was generated thusly:</span>
</pre>
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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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<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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">All binaries were called with --write-ctd and those CTDs were converted to CWL</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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">using https://github.com/WorkflowConversion/CTDConverter</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">lambda-align (1.0.<span class="idiff left right">2-2) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">lambda-align (1.0.<span class="idiff left right">3-1) unstable</span>; urgency=medium</span>
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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="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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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="plaintext"> * Added ref to OMICtools registry.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Fri, 30 Jun 2017 19:04:18 +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * New upstream release fixes Seqan 2.4.0 compat</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Include CWL descriptions</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Run the unit tests and make them available as AutoPkgTests</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Sat, 17 Feb 2018 12:19:04 -0800</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">lambda-align (1.0.2-1) unstable; urgency=medium</span>
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8
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: lambda-align</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Sascha Steinbiss <satta@debian.org>,</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Michael R. Crusoe <michael.crusoe@gmail.com></span>
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2
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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="plaintext">Section: science</span>
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3
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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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Uploaders: Sascha Steinbiss <satta@debian.org></span>
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6
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 10),</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> libseqan2-dev<span class="idiff left right"> (>= 2.2.0+dfsg-2~)</span>,</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> libseqan2-dev,</span>
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8
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> cmake,</span>
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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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> zlib1g-dev,</span>
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10
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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(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="LC10" class="line" lang="plaintext"> libbz2-dev</span>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
11
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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(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="LC11" class="line" lang="plaintext">Standards-Version: 4.0.0</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> libbz2-dev,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> openssl</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.1.3</span>
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12
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/lambda-align.git</span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://anonscm.debian.org/git/debian-med/lambda-align.git</span>
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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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: https://seqan.github.io/lambda</span>
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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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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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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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Package: lambda-align</span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
17
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Suggests: cwl-runner</span>
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19
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Description: Local Aligner for Massive Biological DatA</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> Lambda is a local biosequence aligner optimized for many query sequences</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> and searches in protein space. It is compatible to the de facto standard tool</span>
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<li id="782a36ed6745573288114239783779001929336b">
<a href="https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83#782a36ed6745573288114239783779001929336b"><strong>debian/cwl/lambda.cwl</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/env cwl-runner</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># This CWL file was automatically generated using CTDConverter.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># Visit https://github.com/WorkflowConversion/CTDConverter for more information.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">baseCommand: lambda</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">class: CommandLineTool</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">cwlVersion: v1.0</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">doc: "Lambda is a local aligner optimized for many query sequences and searches in\</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> \ protein space. It is compatible to BLAST, but much faster than BLAST and many\</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> \ other comparable tools.\nDetailed information is available in the wiki: <https://github.com/seqan/lambda/wiki>\n\</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> \n\n\nFor more information, visit http://www.seqan.de"</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">inputs:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">- default: 'false'</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> doc: Display the help message with advanced options.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> id: param_full-help</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> inputBinding:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> prefix: -full-help</span>
</pre>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> label: Display the help message with advanced options.</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> type:</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> - 'null'</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> - string</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">- default: '1'</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> doc: 'Turn this option off to disable version update notifications of the application. '</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> id: param_version-check</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> inputBinding:</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> prefix: -version-check</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> label: 'Turn this option off to disable version update notifications of the application. '</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> type:</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> - 'null'</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> - string</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">- default: 'false'</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> doc: Display long copyright information.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> id: param_copyright</span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> inputBinding:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> prefix: -copyright</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> label: Display long copyright information.</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> type:</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> - 'null'</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> - string</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">- default: '1'</span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> doc: 'Display more/less diagnostic output during operation: 0 [only errors]; 1 [default];</span>
</pre>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> 2 [+run-time, options and statistics].'</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> id: param_verbosity</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> inputBinding:</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> prefix: -verbosity</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> label: 'Display more/less diagnostic output during operation: 0 [only errors]; 1</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> [default]; 2 [+run-time, options and statistics].'</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> type:</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> - 'null'</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> - int</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">- doc: Query sequences.</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> id: param_query</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> inputBinding:</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> prefix: -query</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> label: Query sequences.</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> type: File</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">- doc: Path to original database sequences (a precomputed index with .sa or .fm needs</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> to exist!).</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> id: param_database</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> inputBinding:</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> prefix: -database</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> label: Path to original database sequences (a precomputed index with .sa or .fm</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> needs to exist!).</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> type: File</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">- default: fm</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> doc: database index is in this format.</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> id: param_db-index-type</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> inputBinding:</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> prefix: -db-index-type</span>
</pre>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> label: database index is in this format.</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> type:</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> - 'null'</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> - string</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">- default: output.m8</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> doc: Filename for output output file</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> id: param_output_filename</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> inputBinding:</span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> prefix: -output</span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> label: Filename for output output file</span>
</pre>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> type:</span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> - 'null'</span>
</pre>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> - string</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">- default: std</span>
</pre>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> doc: Print specified column combination and/or order (.m8 and .m9 outputs only);</span>
</pre>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> call -oc help for more details.</span>
</pre>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> id: param_output-columns</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> inputBinding:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> prefix: -output-columns</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> label: Print specified column combination and/or order (.m8 and .m9 outputs only);</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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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="LC91" class="line" lang="plaintext"> call -oc help for more details.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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92
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> type:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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93
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> - 'null'</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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94
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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="LC94" class="line" lang="plaintext"> - string</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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95
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">- default: '0'</span>
</pre>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> doc: Output only matches above this threshold (checked before e-value check).</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> id: param_percent-identity</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> inputBinding:</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> prefix: -percent-identity</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> label: Output only matches above this threshold (checked before e-value check).</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> type:</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> - 'null'</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> - int</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">- default: '0.1'</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> doc: Output only matches that score below this threshold.</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> id: param_e-value</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> inputBinding:</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> prefix: -e-value</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> label: Output only matches that score below this threshold.</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> type:</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> - 'null'</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> - double</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">- default: '500'</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> doc: Print at most this number of matches per query.</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> id: param_num-matches</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> inputBinding:</span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> prefix: -num-matches</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> label: Print at most this number of matches per query.</span>
</pre>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> type:</span>
</pre>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> - 'null'</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> - int</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">- default: 'off'</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> doc: BAM files require all subject names to be written to the header. For SAM this</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> is not required, so Lambda does not automatically do it to save space (especially</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> for protein database this is a lot!). If you still want them with SAM, e.g. for</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> better BAM compatibility, use this option.</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> id: param_sam-with-refheader</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> inputBinding:</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> prefix: -sam-with-refheader</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> label: BAM files require all subject names to be written to the header. For SAM</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> this is not required, so Lambda does not automatically do it to save space (especially</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> for protein database this is a lot!). If you still want them with SAM, e.g. for</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> better BAM compatibility, use this option.</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> type:</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"> - 'null'</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> - string</span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">- default: uniq</span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> doc: Write matching DNA subsequence into SAM/BAM file (BLASTN). For BLASTX and TBLASTX</span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> the matching protein sequence is "untranslated" and positions retransformed to</span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> the original sequence. For BLASTP and TBLASTN there is no DNA sequence so a "*"</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> is written to the SEQ column. The matching protein sequence can be written as</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> an optional tag, see --sam-bam-tags. If set to uniq than the sequence is omitted</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> iff it is identical to the previous match's subsequence.</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"> id: param_sam-bam-seq</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"> inputBinding:</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> prefix: -sam-bam-seq</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> label: Write matching DNA subsequence into SAM/BAM file (BLASTN). For BLASTX and</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> TBLASTX the matching protein sequence is "untranslated" and positions retransformed</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> to the original sequence. For BLASTP and TBLASTN there is no DNA sequence so a</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> "*" is written to the SEQ column. The matching protein sequence can be written</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> as an optional tag, see --sam-bam-tags. If set to uniq than the sequence is omitted</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> iff it is identical to the previous match's subsequence.</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> type:</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> - 'null'</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> - string</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">- default: AS NM ZE ZI ZF</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> doc: Write the specified optional columns to the SAM/BAM file. Call --sam-bam-tags</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> help for more details.</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"> id: param_sam-bam-tags</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"> inputBinding:</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"> prefix: -sam-bam-tags</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> label: Write the specified optional columns to the SAM/BAM file. Call --sam-bam-tags</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> help for more details.</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> type:</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> - 'null'</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> - string</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">- default: hard</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"> doc: Whether to hard-clip or soft-clip the regions beyond the local match. Soft-clipping</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> retains the full sequence in the output file, but obviously uses more space.</span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"> id: param_sam-bam-clip</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"> inputBinding:</span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> prefix: -sam-bam-clip</span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> label: Whether to hard-clip or soft-clip the regions beyond the local match. Soft-clipping</span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"> retains the full sequence in the output file, but obviously uses more space.</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"> type:</span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> - 'null'</span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"> - string</span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">- default: '8'</span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"> doc: number of threads to run concurrently.</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"> id: param_threads</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"> inputBinding:</span>
</pre>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"> prefix: -threads</span>
</pre>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> label: number of threads to run concurrently.</span>
</pre>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> type:</span>
</pre>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"> - 'null'</span>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"> - int</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">- default: none</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> doc: controls double-indexing.</span>
</pre>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"> id: param_query-index-type</span>
</pre>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"> inputBinding:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> prefix: -query-index-type</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"> label: controls double-indexing.</span>
</pre>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"> type:</span>
</pre>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"> - 'null'</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"> - string</span>
</pre>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">- default: blastx</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"> doc: Blast Operation Mode.</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"> id: param_program</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext"> inputBinding:</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"> prefix: -program</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"> label: Blast Operation Mode.</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"> type:</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"> - 'null'</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"> - string</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">- default: '1'</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"> doc: The translation table to use for nucl -> amino acid translation(not for BlastN,</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"> BlastP). See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c for</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext"> ids (default is generic). Six frames are generated.</span>
</pre>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"> id: param_genetic-code</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"> inputBinding:</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"> prefix: -genetic-code</span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"> label: The translation table to use for nucl -> amino acid translation(not for BlastN,</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext"> BlastP). See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c for</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"> ids (default is generic). Six frames are generated.</span>
</pre>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext"> type:</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"> - 'null'</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"> - int</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">- default: murphy10</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"> doc: Alphabet Reduction for seeding phase (ignored for BLASTN).</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"> id: param_alphabet-reduction</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"> inputBinding:</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"> prefix: -alphabet-reduction</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"> label: Alphabet Reduction for seeding phase (ignored for BLASTN).</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"> type:</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"> - 'null'</span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"> - string</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">- default: '10'</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"> doc: Length of the seeds (default = 14 for BLASTN).</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"> id: param_seed-length</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"> inputBinding:</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext"> prefix: -seed-length</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"> label: Length of the seeds (default = 14 for BLASTN).</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> type:</span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"> - 'null'</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> - int</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext">- default: '10'</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"> doc: Offset for seeding (if unset = seed-length, non-overlapping; default = 5 for</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext"> BLASTN).</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext"> id: param_seed-offset</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext"> inputBinding:</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext"> prefix: -seed-offset</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext"> label: Offset for seeding (if unset = seed-length, non-overlapping; default = 5</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext"> for BLASTN).</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"> type:</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext"> - 'null'</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"> - int</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">- default: '1'</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"> doc: maximum seed distance.</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext"> id: param_seed-delta</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext"> inputBinding:</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext"> prefix: -seed-delta</span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext"> label: maximum seed distance.</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext"> type:</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext"> - 'null'</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext"> - int</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext">- default: '2'</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"> doc: evaluate score of a region NUM times the size of the seed before extension</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext"> (0 -> no pre-scoring, 1 -> evaluate seed, n-> area around seed, as well; default</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"> = 1 if no reduction is used).</span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"> id: param_pre-scoring</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"> inputBinding:</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"> prefix: -pre-scoring</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"> label: evaluate score of a region NUM times the size of the seed before extension</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext"> (0 -> no pre-scoring, 1 -> evaluate seed, n-> area around seed, as well; default</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext"> = 1 if no reduction is used).</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext"> type:</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext"> - 'null'</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"> - int</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">- default: '2.0'</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext"> doc: minimum average score per position in pre-scoring region.</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"> id: param_pre-scoring-threshold</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"> inputBinding:</span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext"> prefix: -pre-scoring-threshold</span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext"> label: minimum average score per position in pre-scoring region.</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext"> type:</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext"> - 'null'</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext"> - double</span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">- default: 'on'</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext"> doc: filter hits that will likely duplicate a match already found.</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext"> id: param_filter-putative-duplicates</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext"> inputBinding:</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext"> prefix: -filter-putative-duplicates</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext"> label: filter hits that will likely duplicate a match already found.</span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext"> type:</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext"> - 'null'</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext"> - string</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">- default: 'on'</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext"> doc: If the maximum number of matches per query are found already, stop searching</span>
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<td class="diff-line-num new new_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext"> if the remaining realm looks unfeasable.</span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext"> id: param_filter-putative-abundant</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext"> inputBinding:</span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext"> prefix: -filter-putative-abundant</span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext"> label: If the maximum number of matches per query are found already, stop searching</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext"> if the remaining realm looks unfeasable.</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext"> type:</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext"> - 'null'</span>
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<td class="diff-line-num new new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext"> - string</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">- default: '62'</span>
</pre>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext"> doc: use '45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80; [ignored</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext"> for BlastN]</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext"> id: param_scoring-scheme</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext"> inputBinding:</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext"> prefix: -scoring-scheme</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext"> label: use '45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80; [ignored</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext"> for BlastN]</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext"> type:</span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext"> - 'null'</span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext"> - int</span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">- default: '-1'</span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext"> doc: Score per gap character (default = -2 for BLASTN).</span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext"> id: param_score-gap</span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext"> inputBinding:</span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext"> prefix: -score-gap</span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext"> label: Score per gap character (default = -2 for BLASTN).</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext"> type:</span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext"> - 'null'</span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext"> - int</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">- default: '-11'</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext"> doc: Additional cost for opening gap (default = -5 for BLASTN).</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext"> id: param_score-gap-open</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext"> inputBinding:</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext"> prefix: -score-gap-open</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext"> label: Additional cost for opening gap (default = -5 for BLASTN).</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext"> type:</span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext"> - 'null'</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext"> - int</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">- default: '2'</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext"> doc: Match score [only BLASTN])</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext"> id: param_score-match</span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext"> inputBinding:</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext"> prefix: -score-match</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext"> label: Match score [only BLASTN])</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext"> type:</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext"> - 'null'</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext"> - int</span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">- default: '-3'</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext"> doc: Mismatch score [only BLASTN]</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext"> id: param_score-mismatch</span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext"> inputBinding:</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext"> prefix: -score-mismatch</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext"> label: Mismatch score [only BLASTN]</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext"> type:</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext"> - 'null'</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext"> - int</span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext">- default: '30'</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext"> doc: Stop Banded extension if score x below the maximum seen (-1 means no xdrop).</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext"> id: param_x-drop</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext"> inputBinding:</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext"> prefix: -x-drop</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext"> label: Stop Banded extension if score x below the maximum seen (-1 means no xdrop).</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext"> type:</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext"> - 'null'</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext"> - int</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext">- default: '-3'</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext"> doc: Size of the DP-band used in extension (-3 means log2 of query length; -2 means</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext"> sqrt of query length; -1 means full dp; n means band of size 2n+1)</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext"> id: param_band</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext"> inputBinding:</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext"> prefix: -band</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext"> label: Size of the DP-band used in extension (-3 means log2 of query length; -2</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext"> means sqrt of query length; -1 means full dp; n means band of size 2n+1)</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext"> type:</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext"> - 'null'</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext"> - int</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext">label: the Local Aligner for Massive Biological DatA</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext">outputs:</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext">- doc: File to hold reports on hits (.m* are blastall -m* formats; .m8 is tab-seperated,</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext"> .m9 is tab-seperated with with comments, .m0 is pairwise format).</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext"> id: param_output</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext"> label: File to hold reports on hits (.m* are blastall -m* formats; .m8 is tab-seperated,</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext"> .m9 is tab-seperated with with comments, .m0 is pairwise format).</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext"> outputBinding:</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext"> glob: $(inputs.param_output_filename)</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext"> type:</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext"> - 'null'</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext"> - File</span></pre>
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<a href="https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83#e2a5ec806298fab5b917bf10ca91997dab840655"><strong>debian/cwl/lambda_indexer.cwl</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/env cwl-runner</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># This CWL file was automatically generated using CTDConverter.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># Visit https://github.com/WorkflowConversion/CTDConverter for more information.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">baseCommand: lambda_indexer</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">class: CommandLineTool</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">cwlVersion: v1.0</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">doc: "Lambda is a local aligner optimized for many query sequences and searches in\</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> \ protein space. It is compatible to BLAST, but much faster than BLAST and many\</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> \ other comparable tools.\nDetailed information is available in the wiki: <https://github.com/seqan/lambda/wiki>\n\</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> This is the indexer_binary for creating lambda-compatible databases.\n\n\n\nFor\</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> \ more information, visit http://www.seqan.de"</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">inputs:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">- default: 'false'</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> doc: Display the help message with advanced options.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> id: param_full-help</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> inputBinding:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> prefix: -full-help</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> label: Display the help message with advanced options.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> type:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> - 'null'</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> - string</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">- default: '1'</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> doc: 'Turn this option off to disable version update notifications of the application. '</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> id: param_version-check</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> inputBinding:</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> prefix: -version-check</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> label: 'Turn this option off to disable version update notifications of the application. '</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> type:</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> - 'null'</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> - string</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">- default: 'false'</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> doc: Display long copyright information.</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> id: param_copyright</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> inputBinding:</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> prefix: -copyright</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> label: Display long copyright information.</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> type:</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> - 'null'</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> - string</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">- default: '1'</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> doc: 'Display more/less diagnostic output during operation: 0 [only errors]; 1 [default];</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> 2 [+run-time, options and statistics].'</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> id: param_verbosity</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> inputBinding:</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> prefix: -verbosity</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> label: 'Display more/less diagnostic output during operation: 0 [only errors]; 1</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> [default]; 2 [+run-time, options and statistics].'</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> type:</span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> - 'null'</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> - int</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">- doc: Database sequences.</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> id: param_database</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> inputBinding:</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> prefix: -database</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> label: Database sequences.</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> type: File</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">- doc: SEG intervals for database(optional).</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> id: param_segfile</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> inputBinding:</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> prefix: -segfile</span>
</pre>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> label: SEG intervals for database(optional).</span>
</pre>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> type:</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> - 'null'</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> - File</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">- default: fm</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> doc: Suffix array or full-text minute space.</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> id: param_db-index-type</span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> inputBinding:</span>
</pre>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> prefix: -db-index-type</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> label: Suffix array or full-text minute space.</span>
</pre>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> type:</span>
</pre>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> - 'null'</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> - string</span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">- default: 'on'</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> doc: Truncate IDs at first whitespace. This saves a lot of space and is irrelevant</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> for all LAMBDA output formats other than BLAST Pairwise (.m0).</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> id: param_truncate-ids</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> inputBinding:</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> prefix: -truncate-ids</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> label: Truncate IDs at first whitespace. This saves a lot of space and is irrelevant</span>
</pre>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> for all LAMBDA output formats other than BLAST Pairwise (.m0).</span>
</pre>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> type:</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> - 'null'</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> - string</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">- default: blastx</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> doc: Blast Operation Mode.</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> id: param_program</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> inputBinding:</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> prefix: -program</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> label: Blast Operation Mode.</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> type:</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> - 'null'</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> - string</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">- default: '1'</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> doc: The translation table to use (not for BlastN, BlastP). See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c</span>
</pre>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> for ids (default is generic).</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> id: param_genetic-code</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> inputBinding:</span>
</pre>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> prefix: -genetic-code</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> label: The translation table to use (not for BlastN, BlastP). See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c</span>
</pre>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> for ids (default is generic).</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> type:</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> - 'null'</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> - int</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">- default: murphy10</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> doc: Alphabet Reduction for seeding phase (ignored for BLASTN).</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> id: param_alphabet-reduction</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> inputBinding:</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> prefix: -alphabet-reduction</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> label: Alphabet Reduction for seeding phase (ignored for BLASTN).</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> type:</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> - 'null'</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> - string</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">- default: radixsort</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> doc: Algorithm for SA construction (also used for FM; see Memory Requirements below!).</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> id: param_algorithm</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> inputBinding:</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> prefix: -algorithm</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> label: Algorithm for SA construction (also used for FM; see Memory Requirements</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> below!).</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> type:</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> - 'null'</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> - string</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">- default: '8'</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> doc: number of threads to run concurrently (ignored if a == skew7ext).</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> id: param_threads</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> inputBinding:</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> prefix: -threads</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> label: number of threads to run concurrently (ignored if a == skew7ext).</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> type:</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> - 'null'</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> - int</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">- default: /home/mcrusoe/debian/lambda-align</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> doc: temporary directory used by skew, defaults to working directory.</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> id: param_tmp-dir</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> inputBinding:</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> prefix: -tmp-dir</span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> label: temporary directory used by skew, defaults to working directory.</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> type:</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> - 'null'</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> - string</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">label: indexer for creating lambda-compatible databases</span></pre>
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<a href="https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83#efc7fe57b5983b0283c6410fceef7e74f687aeb5"><strong>debian/lintian-overrides</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># The term 'iff' actually exists and means 'if anf only if'.</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">lambda-align: spelling-error-in-binary usr/bin/lambda iff if</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">lambda-align: spelling-error-in-binary usr/bin/lambda_indexer iff if</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">lambda-align: spelling-error-in-manpage usr/share/man/man1/lambda.1.gz iff if</span></pre>
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<a href="https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83#6f022ae6349b36b113053d3955c70c2276bed7cf"><strong>debian/patches/force-link-rt-pthread.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,9 +2,9 @@ Description: enforce linking of -lrt -lpthread</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> This patch makes sure that these get linked even though they might</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> be missing in $SEQAN_LIBRARIES (until this is fixed in libseqan2-dev).</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff">Author: Sascha Steinbiss <satta@debian.org></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/src/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/src/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -20<span class="idiff left right">7,8 +207</span>,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">lambda-align.orig</span>/src/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">lambda-align</span>/src/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -20<span class="idiff left right">8,8 +208</span>,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> radix_inplace.h)</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"> # Add dependencies found by find_package (SeqAn).</span>
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<a href="https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -25,3 +25,6 @@ override_dh_installman:</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> dh_auto_configure -- -DLAMBDA_NATIVE_BUILD=OFF -DLAMBDA_MMAPPED_DB=ON -DCMAKE_BUILD_TYPE=Release</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> cd build/tests && ctest --parallel $(shell nproc)</span></pre>
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<a href="https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-tests</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: lambda-align, openssl, gzip, coreutils, diffutils</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83#aab2726ed6daf419caf178b1480b6d7da8a85af6"><strong>debian/tests/run-tests</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh -e</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell">mkdir build</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>build</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell">cmake ../</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>binary <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">$(</span>dpkg <span class="nt" style="color: navy;">-L</span> lambda-align<span class="k" style="font-weight: 600;">)</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do </span>ln <span class="nt" style="color: navy;">-s</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">binary</span><span class="k" style="font-weight: 600;">}</span> bin/<span class="p">;</span> <span class="k" style="font-weight: 600;">done</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell">ctest <span class="nt" style="color: navy;">--parallel</span> <span class="k" style="font-weight: 600;">$(</span>nproc<span class="k" style="font-weight: 600;">)</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83#7be417b8ea0a866946b052f8b0de545ebdaf48b3"><strong>src/holders.hpp</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">@@ -385,7 +385,16 @@ public:</td>
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"> <span class="n" style="color: #333;">ArrayGaps</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TAlignRow1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Gaps</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Infix</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Value</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TGlobalHolder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TTransSubjSeqs</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span><span class="p">,</span></span>
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387
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"> <span class="n" style="color: #333;">ArrayGaps</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TDPContext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DPContext</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Value</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TGlobalHolder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TScoreScheme</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span><span class="p">,</span> <span class="n" style="color: #333;">TScoreExtension</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if (SEQAN_VERSION_MINOR < 4)</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TDPContext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DPContext</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Value</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TGlobalHolder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TScoreScheme</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span><span class="p">,</span> <span class="n" style="color: #333;">TScoreExtension</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TCellValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="p">;</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TDPCell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DPCell_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TCellValue</span><span class="p">,</span> <span class="n" style="color: #333;">TScoreExtension</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TTraceValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TraceBitMap_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TCellValue</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span><span class="p">;</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TScoreHost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TDPCell</span><span class="p">,</span> <span class="n" style="color: #333;">Alloc</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">OverAligned</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TTraceHost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TTraceValue</span><span class="p">,</span> <span class="n" style="color: #333;">Alloc</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">OverAligned</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TDPContext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DPContext</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TDPCell</span><span class="p">,</span> <span class="n" style="color: #333;">TTraceValue</span><span class="p">,</span> <span class="n" style="color: #333;">TScoreHost</span><span class="p">,</span> <span class="n" style="color: #333;">TTraceHost</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TAliExtContext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AliExtContext_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TAlignRow0</span><span class="p">,</span> <span class="n" style="color: #333;">TAlignRow1</span><span class="p">,</span> <span class="n" style="color: #333;">TDPContext</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cpp"> <span class="n" style="color: #333;">TAliExtContext</span> <span class="n" style="color: #333;">alignContext</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/lambda-align/compare/4f23d31f46f45d1210693cbc9479bed7245b0215...9c3a2f5c9a29e4b56f468f1393e6e8ec5ca32c83#7552499545cad9fe761b98d5142c0e067cda8faf"><strong>src/options.hpp</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">@@ -420,14 +420,14 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)</td>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Query sequences."</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="cpp"> <span class="n" style="color: #333;">ArgParseArgument</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INPUT_FILE</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="cpp"> <span class="s" style="color: #d14;">"IN"</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="cpp"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"query"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">toCString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">concat</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">getFileExtensions</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SeqFileIn</span></span><span class="p"><span class="idiff">()),</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff right">' '</span></span><span class="p">)));</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"query"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">getFileExtensions</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SeqFileIn</span></span><span class="p"><span class="idiff right">(</span>)));</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">setRequired</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"q"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cpp"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"d"</span><span class="p">,</span> <span class="s" style="color: #d14;">"database"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Path to original database sequences (a precomputed index with .sa or .fm needs to exist!)."</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="cpp"> <span class="n" style="color: #333;">ArgParseArgument</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INPUT_FILE</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"> <span class="s" style="color: #d14;">"IN"</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="cpp"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"database"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">toCString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">concat</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">getFileExtensions</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SeqFileIn</span></span><span class="p"><span class="idiff">()),</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff right">' '</span></span><span class="p">)));</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"database"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">getFileExtensions</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SeqFileIn</span></span><span class="p"><span class="idiff right">(</span>)));</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> <span class="n" style="color: #333;">setRequired</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"d"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"di"</span><span class="p">,</span> <span class="s" style="color: #d14;">"db-index-type"</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1048,7 +1048,7 @@ parseCommandLine(LambdaIndexerOptions & options, int argc, char const ** argv)</td>
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1048
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1048
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<pre style="margin: 0;"> <span id="LC1048" class="line" lang="cpp"> <span class="n" style="color: #333;">ArgParseArgument</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INPUT_FILE</span><span class="p">,</span></span>
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1049
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1049
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<pre style="margin: 0;"> <span id="LC1049" class="line" lang="cpp"> <span class="s" style="color: #d14;">"IN"</span><span class="p">));</span></span>
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1050
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1050
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<pre style="margin: 0;"> <span id="LC1050" class="line" lang="cpp"> <span class="n" style="color: #333;">setRequired</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"database"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1051
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<pre style="margin: 0;">-<span id="LC1051" class="line" lang="cpp"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"database"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">toCString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">concat</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">getFileExtensions</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SeqFileIn</span></span><span class="p"><span class="idiff">()),</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff right">' '</span></span><span class="p">)));</span></span>
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="cpp"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"database"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">getFileExtensions</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SeqFileIn</span></span><span class="p"><span class="idiff right">(</span>)));</span></span>
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1052
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1052
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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="cpp"></span>
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1053
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<pre style="margin: 0;"> <span id="LC1053" class="line" lang="cpp"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"s"</span><span class="p">,</span></span>
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1054
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1054
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<pre style="margin: 0;"> <span id="LC1054" class="line" lang="cpp"> <span class="s" style="color: #d14;">"segfile"</span><span class="p">,</span></span>
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