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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/vsearch">Debian Med / vsearch</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/vsearch/-/commit/7f4a1ea27f911dd65c69c1f9021f56e76fb5f8e0">7f4a1ea2</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-04-24T00:06:18+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix watch URL
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vsearch/-/commit/73d823fa8902a45aba6b95ffab8284e4811bc4e0">73d823fa</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-04-24T00:06:31+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.17.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vsearch/-/commit/fac6c5f691652d61a2b3d1cc1480a211e6ead377">fac6c5f6</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-04-24T00:06:33+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.17.0'
Update to upstream version '2.17.0'
with Debian dir 2e3d3a27ef0393fa383d4f4bb2d6d517078247c9</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vsearch/-/commit/ec00cc2b87f375288fb74e899705cf65eff113c0">ec00cc2b</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-04-24T00:08:00+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
</pre>
</li>
</ul>
<h4>27 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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</li>
<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#e9eacc068eb0149cb6567e67eb35ca6a728c05af">
man/Makefile.am
</a>
</li>
<li class="file-stats">
<a href="#b7ca4efea9812be2ea989e558de10e419bd9cf39">
man/vsearch.1
</a>
</li>
<li class="file-stats">
<a href="#67e794015a01b8816bd16290e5f8538236da8245">
src/Makefile.am
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</li>
<li class="file-stats">
<a href="#851b053a0662a1beacb7e7b0df773bc30f98c900">
src/allpairs.cc
</a>
</li>
<li class="file-stats">
<a href="#55c7453623853a1b38dbd49f5dc20389cd203fe0">
src/chimera.cc
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<li class="file-stats">
<a href="#f39ff334aa80788f730c6c2fa78e9dda01843d21">
src/eestats.cc
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<li class="file-stats">
<a href="#67ef99e491c4bda5d0c47f152cae53d18d7fbcd3">
src/fasta.cc
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<li class="file-stats">
<a href="#da9831bd375e4011e4dc95b4edb9ec2b35d91bb0">
src/fastqjoin.cc
</a>
</li>
<li class="file-stats">
<a href="#6f963d02896322eab19500836bca3f9a22619a35">
src/fastqops.cc
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</li>
<li class="file-stats">
<a href="#66934cf2fb3d65e60500632c125c6324b6bebbec">
src/fastx.cc
</a>
</li>
<li class="file-stats">
<a href="#10eff3279cfc990f0a974eabcc8aa2d695e029f5">
src/fastx.h
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</li>
<li class="file-stats">
<a href="#5158e97b06e3c2eb531bf6a179b392990120db5a">
src/filter.cc
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<li class="file-stats">
<a href="#f8033b5b738e4f851faa382f3ee8786c9fbd889d">
src/getseq.cc
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<li class="file-stats">
<a href="#9c689a31237f70b17e9bac31f42d1b22ea1d59be">
src/mergepairs.cc
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</li>
<li class="file-stats">
<a href="#863c3ef39e4bd150cec0b310a7eb2384b22670a1">
<span class="new-file">
+
src/orient.cc
</span>
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<li class="file-stats">
<a href="#f5a353284fc2c13a1d86de119b77e52c00961dad">
<span class="new-file">
+
src/orient.h
</span>
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</li>
<li class="file-stats">
<a href="#86db155668a2aba91ba2f6297398674549d9252a">
src/otutable.cc
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</li>
<li class="file-stats">
<a href="#7c0ab125929a2525691761258411d8c080de4e02">
src/search.cc
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</li>
<li class="file-stats">
<a href="#38a97b74048ec78f8a80be22b7af7ae63ac895a1">
src/searchexact.cc
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</li>
<li class="file-stats">
<a href="#20b2f8db5b4d6b8a208f67d263ba9782b8d7657e">
src/sintax.cc
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</li>
<li class="file-stats">
<a href="#b0109d980457466d1deec0f79c45e2b54114fdd5">
src/vsearch.cc
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</li>
<li class="file-stats">
<a href="#d5c50f833cab4828d6d2b3f54dda35a42237db09">
src/vsearch.h
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</li>
</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,14 +3,13 @@ language:</td>
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"></span>
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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">os</span><span class="pi">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">linux</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">osx</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">compiler</span><span class="pi">:</span></span>
</pre>
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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">g++</span></span>
</pre>
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<td class="old_line diff-line-num" 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">
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<td class="new_line diff-line-num" 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" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">clang</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"></span>
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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(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="LC13" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;"><span class="idiff left">if [ $TRAVIS_OS_NAME = linux ]; then </span>sudo apt-get install -y ghostscript groff valgrind<span class="idiff right"> ; else brew install ghostscript; brew install valgrind ; fi</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get install -y ghostscript groff valgrind</span></span>
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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"></span>
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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">./autogen.sh</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -4,7 +4,7 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Introduction</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown">The aim of this project is to create an alternative to the <span class="p">[</span><span class="nv" style="color: #008080;">USEARCH</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.drive5.com/usearch/</span><span class="p">)</span> tool developed by Robert C. Edgar (2010). The new tool should:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">The aim of this project is to create an alternative to the <span class="p">[</span><span class="nv" style="color: #008080;">USEARCH</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left right">s</span>://www.drive5.com/usearch/</span><span class="p">)</span> tool developed by Robert C. Edgar (2010). The new tool should:</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="p">*</span> have open source code with an appropriate open source license</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="p">*</span> be free of charge, gratis</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@ We have implemented a tool called VSEARCH which supports *de novo* and reference</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown">VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch), in contrast to USEARCH which by default uses a heuristic seed and extend aligner. This usually results in more accurate alignments and overall improved sensitivity (recall) with VSEARCH, especially for alignments with gaps.</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">VSEARCH binaries</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases/latest</span><span class="p">)</span> are provided for GNU/Linux on three 64-bit processor architectures: x86-64, POWER8 (ppc64le) and ARMv8 (aarch64). Binaries are also provided for MacOS (version 10.9 Mavericks or later) on Intel (x86-64) and Apple Silicon (ARMv8), as well as Windows (64-bit, version 7 or higher, on x86_64). VSEARCH contains dedicated SIMD code for the three processor<span class="idiff left right">s</span> architectures (SSE2/SSSE3, AltiVec/VMX/VSX, Neon).</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">VSEARCH binaries</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases/latest</span><span class="p">)</span> are provided for GNU/Linux on three 64-bit processor architectures: x86-64, POWER8 (ppc64le) and ARMv8 (aarch64). Binaries are also provided for MacOS (version 10.9 Mavericks or later) on Intel (x86-64) and Apple Silicon (ARMv8), as well as Windows (64-bit, version 7 or higher, on x86_64). VSEARCH contains dedicated SIMD code for the three processor architectures (SSE2/SSSE3, AltiVec/VMX/VSX, Neon).</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown">| CPU <span class="se" style="color: #d14;">\ </span>OS | GNU/Linux | MacOS | Windows |</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown">| ------------- | :-----------: | :----: | :-------: |</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -26,7 +26,10 @@ VSEARCH stands for vectorized search, as the tool takes advantage of parallelism</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown">Various packages, plugins and wrappers are also available from other sources - see <span class="p">[</span><span class="nv" style="color: #008080;">below</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch#packages-plugins-and-wrappers</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown">The source code compiles correctly with gcc (versions 4.8 to 9.1) and llvm-clang (3.8 to 9.0). The source code should also compile on <span class="p">[</span><span class="nv" style="color: #008080;">FreeBSD</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.freebsd.org/</span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">NetBSD</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.netbsd.org/</span><span class="p">)</span> systems.</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">The source code compiles correctly with <span class="sb" style="color: #d14;">`gcc`</span> (versions 4.8.5 to 10.2)</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown">and <span class="sb" style="color: #d14;">`llvm-clang`</span> (3.8 to 13.0). The source code should also compile on</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">FreeBSD</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.freebsd.org/</span><span class="p">)</span> and</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">NetBSD</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.netbsd.org/</span><span class="p">)</span> systems.</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown">VSEARCH can directly read input query and database files that are compressed using gzip and bzip2 (.gz and .bz2) if the zlib and bzip2 libraries are available.</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,7 +37,7 @@ Most of the nucleotide based commands and options in USEARCH version 7 are suppo</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Getting Help</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown">If you can't find an answer in the <span class="p">[</span><span class="nv" style="color: #008080;">VSEARCH documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left right">5.2</span>/vsearch_manual.pdf</span><span class="p">)</span>, please visit the <span class="p">[</span><span class="nv" style="color: #008080;">VSEARCH Web Forum</span><span class="p">](</span><span class="sx" style="color: #d14;">https://groups.google.com/forum/#!forum/vsearch-forum</span><span class="p">)</span> to post a question or start a discussion.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown">If you can't find an answer in the <span class="p">[</span><span class="nv" style="color: #008080;">VSEARCH documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left right">7.0</span>/vsearch_manual.pdf</span><span class="p">)</span>, please visit the <span class="p">[</span><span class="nv" style="color: #008080;">VSEARCH Web Forum</span><span class="p">](</span><span class="sx" style="color: #d14;">https://groups.google.com/forum/#!forum/vsearch-forum</span><span class="p">)</span> to post a question or start a discussion.</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Example</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,18 +50,18 @@ In the example below, VSEARCH will identify sequences in the file database.fsa t</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Source distribution**</span> To download the source distribution from a <span class="p">[</span><span class="nv" style="color: #008080;">release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases</span><span class="p">)</span> and build the executable and the documentation, use the following commands:</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="markdown">wget https://github.com/torognes/vsearch/archive/v2.1<span class="idiff left right">5.2</span>.tar.gz</span>
</pre>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown">tar xzf v2.1<span class="idiff left right">5.2</span>.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown">cd vsearch-2.1<span class="idiff left right">5.2</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown">wget https://github.com/torognes/vsearch/archive/v2.1<span class="idiff left right">7.0</span>.tar.gz</span>
</pre>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown">tar xzf v2.1<span class="idiff left right">7.0</span>.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown">cd vsearch-2.1<span class="idiff left right">7.0</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown">./autogen.sh</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown">./configure</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown">make</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown">make install # as root or sudo make install</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown">You may customize the installation directory using the <span class="sb" style="color: #d14;">`--prefix=DIR`</span> option to <span class="sb" style="color: #d14;">`configure`</span>. If the compression libraries <span class="p">[</span><span class="nv" style="color: #008080;">zlib</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.zlib.net</span><span class="p">)</span> and/or <span class="p">[</span><span class="nv" style="color: #008080;">bzip2</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.<span class="idiff left right">bzip.org</span></span><span class="p">)</span> are installed on the system, they will be detected automatically and support for compressed files will be included in vsearch. Support for compressed files may be disabled using the <span class="sb" style="color: #d14;">`--disable-zlib`</span> and <span class="sb" style="color: #d14;">`--disable-bzip2`</span> options to <span class="sb" style="color: #d14;">`configure`</span>. A PDF version of the manual will be created from the <span class="sb" style="color: #d14;">`vsearch.1`</span> manual file if <span class="sb" style="color: #d14;">`ps2pdf`</span> is available, unless disabled using the <span class="sb" style="color: #d14;">`--disable-pdfman`</span> option to <span class="sb" style="color: #d14;">`configure`</span>. Other options may also be applied to <span class="sb" style="color: #d14;">`configure`</span>, please run <span class="sb" style="color: #d14;">`configure -h`</span> to see them all. GNU autoconf (version 2.63 or later), automake and the GCC C++ compiler is required to build vsearch.</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown">You may customize the installation directory using the <span class="sb" style="color: #d14;">`--prefix=DIR`</span> option to <span class="sb" style="color: #d14;">`configure`</span>. If the compression libraries <span class="p">[</span><span class="nv" style="color: #008080;">zlib</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left">s</span>://www.zlib.net</span><span class="p">)</span> and/or <span class="p">[</span><span class="nv" style="color: #008080;">bzip2</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff">s</span>://www.<span class="idiff right">sourceware.org/bzip2/</span></span><span class="p">)</span> are installed on the system, they will be detected automatically and support for compressed files will be included in vsearch. Support for compressed files may be disabled using the <span class="sb" style="color: #d14;">`--disable-zlib`</span> and <span class="sb" style="color: #d14;">`--disable-bzip2`</span> options to <span class="sb" style="color: #d14;">`configure`</span>. A PDF version of the manual will be created from the <span class="sb" style="color: #d14;">`vsearch.1`</span> manual file if <span class="sb" style="color: #d14;">`ps2pdf`</span> is available, unless disabled using the <span class="sb" style="color: #d14;">`--disable-pdfman`</span> option to <span class="sb" style="color: #d14;">`configure`</span>. Other options may also be applied to <span class="sb" style="color: #d14;">`configure`</span>, please run <span class="sb" style="color: #d14;">`configure -h`</span> to see them all. GNU autoconf (version 2.63 or later), automake and the GCC C++ compiler is required to build vsearch.</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown">The Windows binary was compiled using the <span class="p">[</span><span class="nv" style="color: #008080;">Mingw-w64</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left right">s</span>://mingw-w64.org/</span><span class="p">)</span> C++ cross-compiler.</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown">The Windows binary was compiled using the <span class="p">[</span><span class="nv" style="color: #008080;">Mingw-w64</span><span class="p">](</span><span class="sx" style="color: #d14;">http://mingw-w64.org/</span><span class="p">)</span> C++ cross-compiler.</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Cloning the repo**</span> Instead of downloading the source distribution as a compressed archive, you could clone the repo and build it as shown below. The options to <span class="sb" style="color: #d14;">`configure`</span> as described above are still valid.</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -78,43 +81,43 @@ Binary distributions are provided for x86-64 systems running GNU/Linux, macOS (v</td>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown">Download the appropriate executable for your system using the following commands if you are using a Linux x86_64 system:</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left">5.2</span>/vsearch-2.1<span class="idiff right">5.2</span>-linux-x86_64.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.1<span class="idiff left right">5.2</span>-linux-x86_64.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left">7.0</span>/vsearch-2.1<span class="idiff right">7.0</span>-linux-x86_64.tar.gz</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.1<span class="idiff left right">7.0</span>-linux-x86_64.tar.gz</span>
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83
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"><span class="p">```</span></span>
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84
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown"></span>
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85
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown">Or these commands if you are using a Linux ppc64le system:</span>
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86
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="markdown"></span>
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87
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<td class="new_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
</pre>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left">5.2</span>/vsearch-2.1<span class="idiff right">5.2</span>-linux-ppc64le.tar.gz</span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.1<span class="idiff left right">5.2</span>-linux-ppc64le.tar.gz</span>
</pre>
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91
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left">7.0</span>/vsearch-2.1<span class="idiff right">7.0</span>-linux-ppc64le.tar.gz</span>
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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.1<span class="idiff left right">7.0</span>-linux-ppc64le.tar.gz</span>
</pre>
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90
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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91
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown"></span>
</pre>
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92
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<td class="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown">Or these commands if you are using a Linux aarch64 system:</span>
</pre>
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93
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown"></span>
</pre>
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94
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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
</pre>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left">5.2</span>/vsearch-2.1<span class="idiff right">5.2</span>-linux-aarch64.tar.gz</span>
</pre>
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96
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<td class="new_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.1<span class="idiff left right">5.2</span>-linux-aarch64.tar.gz</span>
</pre>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left">7.0</span>/vsearch-2.1<span class="idiff right">7.0</span>-linux-aarch64.tar.gz</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.1<span class="idiff left right">7.0</span>-linux-aarch64.tar.gz</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
97
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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98
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<td class="new_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
101
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
99
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<td class="new_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown">Or these commands if you are using a Mac:</span>
</pre>
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100
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"></span>
</pre>
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101
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
</pre>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left">5.2</span>/vsearch-2.1<span class="idiff right">5.2</span>-macos-x86_64.tar.gz</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.1<span class="idiff left right">5.2</span>-macos-x86_64.tar.gz</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left">7.0</span>/vsearch-2.1<span class="idiff right">7.0</span>-macos-x86_64.tar.gz</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.1<span class="idiff left right">7.0</span>-macos-x86_64.tar.gz</span>
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104
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="markdown">Or if you are using Windows, download and extract (unzip) the contents of this file:</span>
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"></span>
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="markdown">https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left">5.2</span>/vsearch-2.1<span class="idiff right">5.2</span>-win-x86_64.zip</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown">https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left">7.0</span>/vsearch-2.1<span class="idiff right">7.0</span>-win-x86_64.zip</span>
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown"><span class="p">```</span></span>
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="markdown">Linux and Mac: You will now have the binary distribution in a folder called <span class="sb" style="color: #d14;">`vsearch-2.1<span class="idiff left">5.2</span>-linux-x86_64`</span> or <span class="sb" style="color: #d14;">`vsearch-2.1<span class="idiff right">5.2</span>-macos-x86_64`</span> in which you will find three subfolders <span class="sb" style="color: #d14;">`bin`</span>, <span class="sb" style="color: #d14;">`man`</span> and <span class="sb" style="color: #d14;">`doc`</span>. We recommend making a copy or a symbolic link to the vsearch binary <span class="sb" style="color: #d14;">`bin/vsearch`</span> in a folder included in your <span class="sb" style="color: #d14;">`$PATH`</span>, and a copy or a symbolic link to the vsearch man page <span class="sb" style="color: #d14;">`man/vsearch.1`</span> in a folder included in your <span class="sb" style="color: #d14;">`$MANPATH`</span>. The PDF version of the manual is available in <span class="sb" style="color: #d14;">`doc/vsearch_manual.pdf`</span>.</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown">Linux and Mac: You will now have the binary distribution in a folder called <span class="sb" style="color: #d14;">`vsearch-2.1<span class="idiff left">7.0</span>-linux-x86_64`</span> or <span class="sb" style="color: #d14;">`vsearch-2.1<span class="idiff right">7.0</span>-macos-x86_64`</span> in which you will find three subfolders <span class="sb" style="color: #d14;">`bin`</span>, <span class="sb" style="color: #d14;">`man`</span> and <span class="sb" style="color: #d14;">`doc`</span>. We recommend making a copy or a symbolic link to the vsearch binary <span class="sb" style="color: #d14;">`bin/vsearch`</span> in a folder included in your <span class="sb" style="color: #d14;">`$PATH`</span>, and a copy or a symbolic link to the vsearch man page <span class="sb" style="color: #d14;">`man/vsearch.1`</span> in a folder included in your <span class="sb" style="color: #d14;">`$MANPATH`</span>. The PDF version of the manual is available in <span class="sb" style="color: #d14;">`doc/vsearch_manual.pdf`</span>.</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="markdown">Windows: You will now have the binary distribution in a folder called <span class="sb" style="color: #d14;">`vsearch-2.1<span class="idiff left right">5.2</span>-win-x86_64`</span>. The vsearch executable is called <span class="sb" style="color: #d14;">`vsearch.exe`</span>. The manual in PDF format is called <span class="sb" style="color: #d14;">`vsearch_manual.pdf`</span>.</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown">Windows: You will now have the binary distribution in a folder called <span class="sb" style="color: #d14;">`vsearch-2.1<span class="idiff left right">7.0</span>-win-x86_64`</span>. The vsearch executable is called <span class="sb" style="color: #d14;">`vsearch.exe`</span>. The manual in PDF format is called <span class="sb" style="color: #d14;">`vsearch_manual.pdf`</span>.</span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Documentation**</span> The VSEARCH user's manual is available in the <span class="sb" style="color: #d14;">`man`</span> folder in the form of a <span class="p">[</span><span class="nv" style="color: #008080;">man page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/blob/master/man/vsearch.1</span><span class="p">)</span>. A pdf version (<span class="p">[</span><span class="nv" style="color: #008080;">vsearch_manual.pdf</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left">5.2</span>/vsearch_manual.pdf</span><span class="p">)</span>) will be generated by <span class="sb" style="color: #d14;">`make`</span>. To install the manpage manually, copy the <span class="sb" style="color: #d14;">`vsearch.1`</span> file or a create a symbolic link to <span class="sb" style="color: #d14;">`vsearch.1`</span> in a folder included in your <span class="sb" style="color: #d14;">`$MANPATH`</span>. The manual in both formats is also available with the binary distribution. The manual in PDF form (<span class="p">[</span><span class="nv" style="color: #008080;">vsearch_manual.pdf</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff right">5.2</span>/vsearch_manual.pdf</span><span class="p">)</span>) is also attached to the latest <span class="p">[</span><span class="nv" style="color: #008080;">release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Documentation**</span> The VSEARCH user's manual is available in the <span class="sb" style="color: #d14;">`man`</span> folder in the form of a <span class="p">[</span><span class="nv" style="color: #008080;">man page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/blob/master/man/vsearch.1</span><span class="p">)</span>. A pdf version (<span class="p">[</span><span class="nv" style="color: #008080;">vsearch_manual.pdf</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left">7.0</span>/vsearch_manual.pdf</span><span class="p">)</span>) will be generated by <span class="sb" style="color: #d14;">`make`</span>. To install the manpage manually, copy the <span class="sb" style="color: #d14;">`vsearch.1`</span> file or a create a symbolic link to <span class="sb" style="color: #d14;">`vsearch.1`</span> in a folder included in your <span class="sb" style="color: #d14;">`$MANPATH`</span>. The manual in both formats is also available with the binary distribution. The manual in PDF form (<span class="p">[</span><span class="nv" style="color: #008080;">vsearch_manual.pdf</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff right">7.0</span>/vsearch_manual.pdf</span><span class="p">)</span>) is also attached to the latest <span class="p">[</span><span class="nv" style="color: #008080;">release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Packages, plugins, and wrappers</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -127,7 +130,7 @@ Windows: You will now have the binary distribution in a folder called `vsearch-2</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(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="LC131" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Galaxy wrapper**</span> Thanks to the work of the <span class="p">[</span><span class="nv" style="color: #008080;">Intergalactic Utilities Commission</span><span class="p">](</span><span class="sx" style="color: #d14;">https://wiki.galaxyproject.org/IUC</span><span class="p">)</span> members, vsearch is now part of the <span class="p">[</span><span class="nv" style="color: #008080;">Galaxy ToolShed</span><span class="p">](</span><span class="sx" style="color: #d14;">https://toolshed.g2.bx.psu.edu/view/iuc/vsearch/</span><span class="p">)</span>.</span>
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129
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Homebrew package**</span> Thanks to <span class="p">[</span><span class="nv" style="color: #008080;">Torsten Seeman</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/tseemann</span><span class="p">)</span>, a <span class="p">[</span><span class="nv" style="color: #008080;">vsearch package</span><span class="p">](</span><span class="sx" style="color: #d14;">https://<span class="idiff left right">github.com/Homebrew/homebrew-science/pull/2409</span></span><span class="p">)</span> for <span class="p">[</span><span class="nv" style="color: #008080;">Homebrew</span><span class="p">](</span><span class="sx" style="color: #d14;">http://brew.sh/</span><span class="p">)</span> has been made.</span>
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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Homebrew package**</span> Thanks to <span class="p">[</span><span class="nv" style="color: #008080;">Torsten Seeman</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/tseemann</span><span class="p">)</span>, a <span class="p">[</span><span class="nv" style="color: #008080;">vsearch package</span><span class="p">](</span><span class="sx" style="color: #d14;">https://<span class="idiff left right">formulae.brew.sh/formula/vsearch</span></span><span class="p">)</span> for <span class="p">[</span><span class="nv" style="color: #008080;">Homebrew</span><span class="p">](</span><span class="sx" style="color: #d14;">http://brew.sh/</span><span class="p">)</span> has been made.</span>
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131
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<td class="new_line diff-line-num" data-linenumber="134" style="width: 35px; color: rgba(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="LC134" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
132
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Pkgsrc package**</span> Thanks to <span class="p">[</span><span class="nv" style="color: #008080;">Jason Bacon</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/outpaddling</span><span class="p">)</span>, a vsearch <span class="p">[</span><span class="nv" style="color: #008080;">pkgsrc</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.pkgsrc.org</span><span class="p">)</span> package is available for NetBSD and other UNIX-like systems. Install the binary package with <span class="sb" style="color: #d14;">`pkgin install vsearch`</span>, or build from source with additional optimizations.</span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -171,7 +174,7 @@ The VSEARCH code is dual-licensed either under the GNU General Public License ve</td>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(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="LC175" class="line" lang="markdown">VSEARCH includes code from several other projects. We thank the authors for making their source code available.</span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(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="LC174" class="line" lang="markdown">VSEARCH includes code from Google's <span class="p">[</span><span class="nv" style="color: #008080;">CityHash project</span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff left">code.google.com/p</span>/cityhash<span class="idiff right">/</span></span><span class="p">)</span> by Geoff Pike and Jyrki Alakuijala, providing some excellent hash functions available under a MIT license.</span>
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<td class="new_line diff-line-num new" 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">
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="markdown">VSEARCH includes code from Google's <span class="p">[</span><span class="nv" style="color: #008080;">CityHash project</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left">s</span>://<span class="idiff right">github.com/google</span>/cityhash</span><span class="p">)</span> by Geoff Pike and Jyrki Alakuijala, providing some excellent hash functions available under a MIT license.</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
175
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<td class="new_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(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="LC178" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num" data-linenumber="176" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="markdown">VSEARCH includes code derived from Tatusov and Lipman's DUST program that is in the public domain.</span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -181,9 +184,9 @@ VSEARCH includes public domain code written by Steve Reid and others for the SHA</td>
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="markdown">The VSEARCH distribution includes code from GNU Autoconf which normally is available under the GNU General Public License, but may be distributed with the special autoconf configure script exception.</span>
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="markdown"></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="markdown">VSEARCH may include code from the <span class="p">[</span><span class="nv" style="color: #008080;">zlib</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.zlib.net</span><span class="p">)</span> library copyright Jean-loup Gailly and Mark Adler, distributed under the <span class="p">[</span><span class="nv" style="color: #008080;">zlib license</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.zlib.net/zlib_license.html</span><span class="p">)</span>.</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="markdown">VSEARCH may include code from the <span class="p">[</span><span class="nv" style="color: #008080;">zlib</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left">s</span>://www.zlib.net</span><span class="p">)</span> library copyright Jean-loup Gailly and Mark Adler, distributed under the <span class="p">[</span><span class="nv" style="color: #008080;">zlib license</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff right">s</span>://www.zlib.net/zlib_license.html</span><span class="p">)</span>.</span>
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185
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="markdown">VSEARCH may include code from the <span class="p">[</span><span class="nv" style="color: #008080;">bzip2</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.<span class="idiff left right">bzip.org</span></span><span class="p">)</span> library copyright Julian R. Seward, distributed under a BSD-style license.</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="markdown">VSEARCH may include code from the <span class="p">[</span><span class="nv" style="color: #008080;">bzip2</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left">s</span>://www.<span class="idiff right">sourceware.org/bzip2/</span></span><span class="p">)</span> library copyright Julian R. Seward, distributed under a BSD-style license.</span>
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187
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="markdown"></span>
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="markdown"></span>
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189
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Code</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -223,6 +226,7 @@ File | Description</td>
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223
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**mergepairs.cc**</span> | Paired-end read merging</span>
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224
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**minheap.cc**</span> | A minheap implementation for the list of top kmer matches</span>
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225
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**msa.cc**</span> | Simple multiple sequence alignment and consensus sequence computation for clusters</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**orient.cc**</span> | Orient direction of sequences based on reference database</span>
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226
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**otutable.cc**</span> | Generate OTU tables in various formats</span>
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227
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**rerep.cc**</span> | Rereplication</span>
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228
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**results.cc**</span> | Output results in various formats (alnout, userout, blast6, uc)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -243,7 +247,7 @@ File | Description</td>
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243
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**vsearch.cc**</span> | Main program file, general initialization, reads arguments and parses options, writes info.</span>
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**xstring.h**</span> | Code for a simple string class</span>
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="markdown">VSEARCH may be compiled with zlib or bzip2 integration that allows it to read compressed FASTA files. The <span class="p">[</span><span class="nv" style="color: #008080;">zlib</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.zlib.net/</span><span class="p">)</span> and the <span class="p">[</span><span class="nv" style="color: #008080;">bzip2</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.<span class="idiff left right">bzip.org</span>/</span><span class="p">)</span> libraries are needed for this.</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="markdown">VSEARCH may be compiled with zlib or bzip2 integration that allows it to read compressed FASTA files. The <span class="p">[</span><span class="nv" style="color: #008080;">zlib</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.zlib.net/</span><span class="p">)</span> and the <span class="p">[</span><span class="nv" style="color: #008080;">bzip2</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left">s</span>://www.<span class="idiff right">sourceware.org/bzip2</span>/</span><span class="p">)</span> libraries are needed for this.</span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Bugs</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -294,9 +298,9 @@ Please note that citing any of the underlying algorithms, e.g. UCHIME, may also</td>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="markdown">Test datasets (found in the separate vsearch-data repository) were</span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="markdown">obtained from</span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="markdown">the <span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: #008080;">BioMarks project</span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">http://biomarks.eu/</span></span><span class="p"><span class="idiff right">)</span></span> <span class="p">(</span><span class="sx" style="color: #d14;">Logares</span> et al. 2014),</span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="markdown">the <span class="p">[</span><span class="nv" style="color: #008080;">TARA OCEANS project</span><span class="p">](</span><span class="sx" style="color: #d14;">http://oceans.taraexpeditions.org/</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">Karsenti</span> et al. 2011)</span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="markdown">and the <span class="p">[</span><span class="nv" style="color: #008080;">Protist Ribosomal <span class="idiff left">Database</span></span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff">ssu-rrna.org/</span></span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">Guillou</span> et al. 201<span class="idiff right">2</span>).</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="markdown">the BioMarks project (Logares et al. 2014),</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="markdown">the <span class="p">[</span><span class="nv" style="color: #008080;">TARA OCEANS project</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left">s</span>://oceans.taraexpeditions.org/<span class="idiff right">en/</span></span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">Karsenti</span> et al. 2011)</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="markdown">and the <span class="p">[</span><span class="nv" style="color: #008080;">Protist Ribosomal <span class="idiff left">Reference Database (PR<sup>2</sup>)</span></span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff">s</span>://<span class="idiff">github.com/pr2database/pr2database</span></span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">Guillou</span> et al. 201<span class="idiff right">3</span>).</span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## References</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -304,28 +308,28 @@ and the [Protist Ribosomal Database](http://ssu-rrna.org/) (Guillou et al. 2012)</td>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="markdown"><span class="p">*</span> Edgar RC (2010)</span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Search and clustering orders of magnitude faster than BLAST.**</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Bioinformatics*</span>, 26 (19): 2460-2461.</span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="markdown">doi:<span class="p">[</span><span class="nv" style="color: #008080;">10.1093/bioinformatics/btq461</span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff left right">dx.</span>doi.org/10.1093/bioinformatics/btq461</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="markdown">doi:<span class="p">[</span><span class="nv" style="color: #008080;">10.1093/bioinformatics/btq461</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left right">s</span>://doi.org/10.1093/bioinformatics/btq461</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="markdown"><span class="p">*</span> Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011)</span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**UCHIME improves sensitivity and speed of chimera detection.**</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Bioinformatics*</span>, 27 (16): 2194-2200.</span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="markdown">doi:<span class="p">[</span><span class="nv" style="color: #008080;">10.1093/bioinformatics/btr381</span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff left right">dx.</span>doi.org/10.1093/bioinformatics/btr381</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="markdown">doi:<span class="p">[</span><span class="nv" style="color: #008080;">10.1093/bioinformatics/btr381</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left right">s</span>://doi.org/10.1093/bioinformatics/btr381</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="markdown"><span class="p">*</span> Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, Boutte C, Burgaud G, de Vargas C, Decelle J, del Campo J, Dolan J, Dunthorn M, Edvardsen B, Holzmann M, Kooistra W, Lara E, Lebescot N, Logares R, Mahé F, Massana R, Montresor M, Morard R, Not F, Pawlowski J, Probert I, Sauvadet A-L, Siano R, Stoeck T, Vaulot D, Zimmermann P & Christen R (2013)</span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy.**</span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Nucleic Acids Research*</span>, 41 (D1), D597-D604.</span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="markdown">doi:<span class="p">[</span><span class="nv" style="color: #008080;">10.1093/nar/gks1160</span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff left right">dx.</span>doi.org/10.1093/nar/gks1160</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="markdown">doi:<span class="p">[</span><span class="nv" style="color: #008080;">10.1093/nar/gks1160</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left right">s</span>://doi.org/10.1093/nar/gks1160</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="markdown"><span class="p">*</span> Karsenti E, González Acinas S, Bork P, Bowler C, de Vargas C, Raes J, Sullivan M B, Arendt D, Benzoni F, Claverie J-M, Follows M, Jaillon O, Gorsky G, Hingamp P, Iudicone D, Kandels-Lewis S, Krzic U, Not F, Ogata H, Pesant S, Reynaud E G, Sardet C, Sieracki M E, Speich S, Velayoudon D, Weissenbach J, Wincker P & the Tara Oceans Consortium (2011)</span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**A holistic approach to marine eco-systems biology.**</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*PLoS Biology*</span>, 9(10), e1001177.</span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="markdown">doi:<span class="p">[</span><span class="nv" style="color: #008080;">10.1371/journal.pbio.1001177</span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff left right">dx.</span>doi.org/10.1371/journal.pbio.1001177</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="markdown">doi:<span class="p">[</span><span class="nv" style="color: #008080;">10.1371/journal.pbio.1001177</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left right">s</span>://doi.org/10.1371/journal.pbio.1001177</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="markdown"><span class="p">*</span> Logares R, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie J-M, Decelle J, Dolan J R, Dunthorn M, Edvardsen B, Gobet A, Kooistra W H C F, Mahé F, Not F, Ogata H, Pawlowski J, Pernice M C, Romac S, Shalchian-Tabrizi K, Simon N, Stoeck T, Santini S, Siano R, Wincker P, Zingone A, Richards T, de Vargas C & Massana R (2014) <span class="gs" style="font-weight: 600;">**The patterning of rare and abundant community assemblages in coastal marine-planktonic microbial eukaryotes.**</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Current Biology*</span>, 24(8), 813-821.</span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="markdown">doi:<span class="p">[</span><span class="nv" style="color: #008080;">10.1016/j.cub.2014.02.050</span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff left right">dx.</span>doi.org/10.1016/j.cub.2014.02.050</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="markdown">doi:<span class="p">[</span><span class="nv" style="color: #008080;">10.1016/j.cub.2014.02.050</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left right">s</span>://doi.org/10.1016/j.cub.2014.02.050</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="markdown"><span class="p">*</span> Rognes T (2011)</span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Faster Smith-Waterman database searches by inter-sequence SIMD parallelisation.**</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*BMC Bioinformatics*</span>, 12: 221.</span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="markdown">doi:<span class="p">[</span><span class="nv" style="color: #008080;">10.1186/1471-2105-12-221</span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff left right">dx.</span>doi.org/10.1186/1471-2105-12-221</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="markdown">doi:<span class="p">[</span><span class="nv" style="color: #008080;">10.1186/1471-2105-12-221</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left right">s</span>://doi.org/10.1186/1471-2105-12-221</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</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">@@ -2,7 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"># Process this file with autoconf to produce a configure script.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AC_PREREQ([2.63])</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">AC_INIT([vsearch], [2.1<span class="idiff left right">5.2</span>], [torognes@ifi.uio.no], [vsearch], [https://github.com/torognes/vsearch])</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">AC_INIT([vsearch], [2.1<span class="idiff left right">7.0</span>], [torognes@ifi.uio.no], [vsearch], [https://github.com/torognes/vsearch])</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">AC_CANONICAL_TARGET</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">AM_INIT_AUTOMAKE([subdir-objects])</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">AC_LANG([C++])</span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">vsearch (2.17.0-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Steffen Möller ]</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Update metadata - added guix, fixed indent</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"> [ Nilesh Patra ]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Fix watch URL</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * New upstream version 2.17.0</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Sat, 24 Apr 2021 00:07:29 +0530</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">vsearch (2.15.2-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</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">opts="downloadurlmangle=s/\/tree\/(.*)/\/archive\/$1.tar.gz/" \</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> https://github.com/torognes/vsearch/releases .*/archive/v([0-9.rc-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/torognes/vsearch/releases .*/archive/<span class="idiff left right">.*/</span>v([0-9.rc-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#e9eacc068eb0149cb6567e67eb35ca6a728c05af"><strong>man/Makefile.am</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,11 +11,7 @@ doc_DATA += vsearch_manual.html</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="nl">vsearch_manual.html </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">vsearch.1</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\\-/-/g'</span> <span class="nv" style="color: #008080;">$<</span> | <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">$(uname)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"Darwin"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="make"> iconv <span class="nt" style="color: #000080;">-f</span> UTF-8 <span class="nt" style="color: #000080;">-t</span> ISO-8859-1 <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="make"> <span class="k" style="font-weight: 600;">else</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cat</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span> | <span class="se" style="color: #d14;">\</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"> iconv <span class="nt" style="color: #000080;">-f</span> UTF-8 <span class="nt" style="color: #000080;">-t</span> ISO-8859-1 | <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"> groff <span class="nt" style="color: #000080;">-t</span> <span class="nt" style="color: #000080;">-m</span> mandoc <span class="nt" style="color: #000080;">-m</span> www <span class="nt" style="color: #000080;">-Thtml</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$@</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="nv" style="color: #008080;">CLEANFILES</span> <span class="o" style="font-weight: 600;">+=</span> vsearch_manual.html</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,11 +25,7 @@ doc_DATA += vsearch_manual.pdf</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"><span class="nl">vsearch_manual.pdf </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">vsearch.1</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\\-/-/g'</span> <span class="nv" style="color: #008080;">$<</span> | <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">$(uname)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"Darwin"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="make"> iconv <span class="nt" style="color: #000080;">-f</span> UTF-8 <span class="nt" style="color: #000080;">-t</span> ISO-8859-1 <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="make"> <span class="k" style="font-weight: 600;">else</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cat</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span> | <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="make"> iconv <span class="nt" style="color: #000080;">-f</span> UTF-8 <span class="nt" style="color: #000080;">-t</span> ISO-8859-1 | <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="make"> groff <span class="nt" style="color: #000080;">-W</span> space <span class="nt" style="color: #000080;">-t</span> <span class="nt" style="color: #000080;">-m</span> mandoc <span class="nt" style="color: #000080;">-T</span> ps <span class="nt" style="color: #000080;">-P</span> <span class="nt" style="color: #000080;">-pa4</span> | ps2pdf - <span class="nv" style="color: #008080;">$@</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"><span class="nv" style="color: #008080;">CLEANFILES</span> <span class="o" style="font-weight: 600;">+=</span> vsearch_manual.pdf</span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#b7ca4efea9812be2ea989e558de10e419bd9cf39"><strong>man/vsearch.1</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" ============================================================================</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH vsearch 1 "<span class="idiff left">January</span> 2<span class="idiff">6</span>, 2021" "version 2.1<span class="idiff right">5.2</span>" "USER COMMANDS"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH vsearch 1 "<span class="idiff left">March</span> 2<span class="idiff">9</span>, 2021" "version 2.1<span class="idiff right">7.0</span>" "USER COMMANDS"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.\" ============================================================================</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">vsearch \(em chimera detection, clustering, dereplication and</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -109,6 +109,13 @@ Masking:</td>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext">\fIoutputfile\fR [\fIoptions\fR]</span>
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext">.PP</span>
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111
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext">.RE</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">Orienting:</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">.RS</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">\fBvsearch\fR \-\-orient \fIfastxfile\fR \-\-db \fIfastafile\fR</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">(\-\-fastaout | \-\-fastqout | \-\-notmatched | \-\-tabbedout)</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">\fIoutputfile\fR [\fIoptions\fR]</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">.PP</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">.RE</span>
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112
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext">Pairwise alignment:</span>
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113
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext">.RS</span>
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114
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">\fBvsearch\fR \-\-allpairs_global \fIfastafile\fR (\-\-alnout |</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1562,12 +1569,12 @@ ambiguous bases (N's), as specified with the \-\-fastq_maxns are also</td>
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1562
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1569
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<pre style="margin: 0;"> <span id="LC1569" class="line" lang="plaintext">discarded (no limit by default). Staggered reads are not merged unless</span>
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1563
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1570
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<pre style="margin: 0;"> <span id="LC1570" class="line" lang="plaintext">the \-\-fastq_allowmergestagger option is specified. The minimum</span>
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1564
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1571
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<pre style="margin: 0;"> <span id="LC1571" class="line" lang="plaintext">length of the overlap region between the reads may be specified with</span>
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1565
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<td class="new_line diff-line-num old" data-linenumber="1572" style="width: 35px; color: rgba(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="LC1565" class="line" lang="plaintext">the \-\-fastq_minovlen option (default 10). The overlap<span class="idiff left right"> region may not</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1566
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<td class="new_line diff-line-num old" data-linenumber="1572" style="width: 35px; color: rgba(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="LC1566" class="line" lang="plaintext">include more mismatches than specified with the<span class="idiff left right"> \-\-fastq_maxdiffs</span></span>
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1567
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<td class="new_line diff-line-num old" data-linenumber="1572" style="width: 35px; color: rgba(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="LC1567" class="line" lang="plaintext">option (10 by default) or a higher percentage of<span class="idiff left right"> mismatches than</span></span>
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1568
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<pre style="margin: 0;">-<span id="LC1568" class="line" lang="plaintext">specified with the \-\-fastq_maxdiffpct option (100.0%<span class="idiff left right"> by default),</span></span>
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1569
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<pre style="margin: 0;">-<span id="LC1569" class="line" lang="plaintext">otherwise the read pair is discarded. Additional rules<span class="idiff left right"> will avoid</span></span>
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1570
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<pre style="margin: 0;">-<span id="LC1570" class="line" lang="plaintext">merging of reads that cannot be aligned reliably and</span>
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1572
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<pre style="margin: 0;">+<span id="LC1572" class="line" lang="plaintext">the \-\-fastq_minovlen option (<span class="idiff left right">at least 5, </span>default 10). The overlap</span>
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1573
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<pre style="margin: 0;">+<span id="LC1573" class="line" lang="plaintext"><span class="idiff left right">region may not </span>include more mismatches than specified with the</span>
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1574
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<pre style="margin: 0;">+<span id="LC1574" class="line" lang="plaintext"><span class="idiff left right">\-\-fastq_maxdiffs </span>option (10 by default) or a higher percentage of</span>
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1575
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<pre style="margin: 0;">+<span id="LC1575" class="line" lang="plaintext"><span class="idiff left right">mismatches than </span>specified with the \-\-fastq_maxdiffpct option (100.0%</span>
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1576
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<pre style="margin: 0;">+<span id="LC1576" class="line" lang="plaintext"><span class="idiff left right">by default), </span>otherwise the read pair is discarded. Additional rules</span>
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1577
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<pre style="margin: 0;">+<span id="LC1577" class="line" lang="plaintext"><span class="idiff left right">will avoid </span>merging of reads that cannot be aligned reliably and</span>
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1571
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1578
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<pre style="margin: 0;"> <span id="LC1578" class="line" lang="plaintext">unambiguously. The mimimum and maximum length of the merged sequence</span>
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1572
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1579
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<pre style="margin: 0;"> <span id="LC1579" class="line" lang="plaintext">may be specified with the \-\-fastq_minmergelen and</span>
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1573
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1580
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<pre style="margin: 0;"> <span id="LC1580" class="line" lang="plaintext">\-\-fastq_maxmergelen options, respectively. The quality value limits</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1591,7 +1598,7 @@ merged sequence. The default is 1.</td>
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1591
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1598
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<pre style="margin: 0;"> <span id="LC1598" class="line" lang="plaintext">.TP</span>
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1592
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1599
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<pre style="margin: 0;"> <span id="LC1599" class="line" lang="plaintext">.BI \-\-fastq_minovlen\~ "positive integer"</span>
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1593
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1600
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<pre style="margin: 0;"> <span id="LC1600" class="line" lang="plaintext">When using \-\-fastq_mergepairs, specify the minimum overlap between</span>
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1594
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<pre style="margin: 0;">-<span id="LC1594" class="line" lang="plaintext">the merged reads. The default is 10.</span>
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1601
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<pre style="margin: 0;">+<span id="LC1601" class="line" lang="plaintext">the merged reads. The default is 10.<span class="idiff left right"> Must be at least 5.</span></span>
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1595
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1602
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<pre style="margin: 0;"> <span id="LC1602" class="line" lang="plaintext">.TAG fastq_nostagger</span>
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1596
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1603
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<pre style="margin: 0;"> <span id="LC1603" class="line" lang="plaintext">.TP</span>
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1597
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1604
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<pre style="margin: 0;"> <span id="LC1604" class="line" lang="plaintext">.B \-\-fastq_nostagger</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2057,6 +2064,67 @@ mask.</td>
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2057
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2064
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<pre style="margin: 0;"> <span id="LC2064" class="line" lang="plaintext">.RE</span>
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2058
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2065
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<pre style="margin: 0;"> <span id="LC2065" class="line" lang="plaintext">.PP</span>
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2059
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2066
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<pre style="margin: 0;"> <span id="LC2066" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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2067
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<pre style="margin: 0;">+<span id="LC2067" class="line" lang="plaintext">.TAG orienting-options</span>
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2068
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<pre style="margin: 0;">+<span id="LC2068" class="line" lang="plaintext">Orienting options:</span>
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2069
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<pre style="margin: 0;">+<span id="LC2069" class="line" lang="plaintext">.RS</span>
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2070
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<pre style="margin: 0;">+<span id="LC2070" class="line" lang="plaintext">.PP</span>
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2071
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<pre style="margin: 0;">+<span id="LC2071" class="line" lang="plaintext">The \-\-orient command can be used to orient the sequences in a given</span>
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2072
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<pre style="margin: 0;">+<span id="LC2072" class="line" lang="plaintext">file in either the forward or the reverse complementary direction</span>
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2073
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<pre style="margin: 0;">+<span id="LC2073" class="line" lang="plaintext">based on a reference database specified with the \-\-db option. The</span>
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2074
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<pre style="margin: 0;">+<span id="LC2074" class="line" lang="plaintext">two strands of each input sequence are compared to the reference</span>
</pre>
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2075
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<pre style="margin: 0;">+<span id="LC2075" class="line" lang="plaintext">database using nucleotide words. If one of the strands share many more</span>
</pre>
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2076
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<pre style="margin: 0;">+<span id="LC2076" class="line" lang="plaintext">words with at least one sequence in the database than the other, that</span>
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2077
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<pre style="margin: 0;">+<span id="LC2077" class="line" lang="plaintext">strand is chosen. The correctly oriented sequences may be written to a</span>
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2078
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<pre style="margin: 0;">+<span id="LC2078" class="line" lang="plaintext">FASTA file specified with the \-\-fastaout, and to a FASTQ file</span>
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<td class="new_line diff-line-num new" data-linenumber="2079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2079
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<pre style="margin: 0;">+<span id="LC2079" class="line" lang="plaintext">specified with the \-\-fastqout option (as long as the input was also</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2080
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<pre style="margin: 0;">+<span id="LC2080" class="line" lang="plaintext">in FASTA format). If the result is uncertain, because the number of</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2081
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<pre style="margin: 0;">+<span id="LC2081" class="line" lang="plaintext">matching words is too similar, the original sequence is written to the</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2082
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<pre style="margin: 0;">+<span id="LC2082" class="line" lang="plaintext">file specified with the \-\-notmatched option. The results may also be</span>
</pre>
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2083
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<pre style="margin: 0;">+<span id="LC2083" class="line" lang="plaintext">written to a tab-delimited text file specified with the \-\-tabbedout</span>
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<td class="new_line diff-line-num new" data-linenumber="2084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2084
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<pre style="margin: 0;">+<span id="LC2084" class="line" lang="plaintext">option. This file will contain the query label, the direction (+, - or</span>
</pre>
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2085
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<pre style="margin: 0;">+<span id="LC2085" class="line" lang="plaintext">?), the number of matching words on the forward strand, and the number</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2086
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<pre style="margin: 0;">+<span id="LC2086" class="line" lang="plaintext">of matching words on the reverse complementary strand. By default, a</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2087
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<pre style="margin: 0;">+<span id="LC2087" class="line" lang="plaintext">word length of 12 is used for this command. The word length may be</span>
</pre>
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2088
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<pre style="margin: 0;">+<span id="LC2088" class="line" lang="plaintext">adjusted using the \-\-wordlength option. There has to be at least 4</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2089
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<pre style="margin: 0;">+<span id="LC2089" class="line" lang="plaintext">times as many matches on one strand than the other for a strand to be</span>
</pre>
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2090
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<pre style="margin: 0;">+<span id="LC2090" class="line" lang="plaintext">selected. In addition to the common options, the following options may</span>
</pre>
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2091
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<pre style="margin: 0;">+<span id="LC2091" class="line" lang="plaintext">also be specified for this command: \-\-dbmask, \-\-qmask,</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2092
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<pre style="margin: 0;">+<span id="LC2092" class="line" lang="plaintext">\-\-relabel, \-\-relabel_keep, \-\-relabel_md5, \-\-relabel_self,</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2093
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<pre style="margin: 0;">+<span id="LC2093" class="line" lang="plaintext">\-\-relabel_sha1, \-\-sizein, and \-\-sizeout.</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2094
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<pre style="margin: 0;">+<span id="LC2094" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2095
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<pre style="margin: 0;">+<span id="LC2095" class="line" lang="plaintext">.TAG db</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2096
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<pre style="margin: 0;">+<span id="LC2096" class="line" lang="plaintext">.TP 9</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2097
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<pre style="margin: 0;">+<span id="LC2097" class="line" lang="plaintext">.BI \-\-db \0filename</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2098
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<pre style="margin: 0;">+<span id="LC2098" class="line" lang="plaintext">Read the reference database from the given file. It may be in FASTA,</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2099
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<pre style="margin: 0;">+<span id="LC2099" class="line" lang="plaintext">FASTQ or UDB format. If an UDB file is used it should have been</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2100
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<pre style="margin: 0;">+<span id="LC2100" class="line" lang="plaintext">created with a wordlength of 12.</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2101
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<pre style="margin: 0;">+<span id="LC2101" class="line" lang="plaintext">.TAG fastaout</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2102
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<pre style="margin: 0;">+<span id="LC2102" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2103
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<pre style="margin: 0;">+<span id="LC2103" class="line" lang="plaintext">.BI \-\-fastaout \0filename</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2104
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2104" class="line" lang="plaintext">Write the correctly oriented sequences to \fIfilename\fR, in fasta format.</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2105
</td>
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<pre style="margin: 0;">+<span id="LC2105" class="line" lang="plaintext">.TAG fastqout</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2106
</td>
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<pre style="margin: 0;">+<span id="LC2106" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2107
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2107" class="line" lang="plaintext">.BI \-\-fastqout \0filename</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2108
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2108" class="line" lang="plaintext">Write the correctly oriented sequences to \fIfilename\fR, in fastq format.</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2109
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<pre style="margin: 0;">+<span id="LC2109" class="line" lang="plaintext">.TAG notmatched</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2110
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<pre style="margin: 0;">+<span id="LC2110" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2111
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<pre style="margin: 0;">+<span id="LC2111" class="line" lang="plaintext">.BI \-\-notmatched \0filename</span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2112
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<pre style="margin: 0;">+<span id="LC2112" class="line" lang="plaintext">Write the sequences with undetermined direction to \fIfilename\fR, in</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2113
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<pre style="margin: 0;">+<span id="LC2113" class="line" lang="plaintext">the orginal format.</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2114
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<pre style="margin: 0;">+<span id="LC2114" class="line" lang="plaintext">.TAG orient</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2115
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<pre style="margin: 0;">+<span id="LC2115" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2116
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<pre style="margin: 0;">+<span id="LC2116" class="line" lang="plaintext">.BI \-\-orient \0filename</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2117
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<pre style="margin: 0;">+<span id="LC2117" class="line" lang="plaintext">Orient the sequences in the given file.</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2118
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<pre style="margin: 0;">+<span id="LC2118" class="line" lang="plaintext">.TAG tabbedout</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2119
</td>
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<pre style="margin: 0;">+<span id="LC2119" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2120
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<pre style="margin: 0;">+<span id="LC2120" class="line" lang="plaintext">.BI \-\-tabbedout \0 filename</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2121
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<pre style="margin: 0;">+<span id="LC2121" class="line" lang="plaintext">Write the resuls to a tab-delimited text file with the specified</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2122
</td>
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<pre style="margin: 0;">+<span id="LC2122" class="line" lang="plaintext">filename. This file will contain the query label, the direction (+, -</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="2123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2123
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<pre style="margin: 0;">+<span id="LC2123" class="line" lang="plaintext">or ?), the number of matching words on the forward strand, and the</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="2124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2124
</td>
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<pre style="margin: 0;">+<span id="LC2124" class="line" lang="plaintext">number of matching words on the reverse complementary strand.</span>
</pre>
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2125
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<pre style="margin: 0;">+<span id="LC2125" class="line" lang="plaintext">.RE</span>
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2126
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<pre style="margin: 0;">+<span id="LC2126" class="line" lang="plaintext">.PP</span>
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2127
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<pre style="margin: 0;">+<span id="LC2127" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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2060
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2128
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<pre style="margin: 0;"> <span id="LC2128" class="line" lang="plaintext">.TAG restriction-site-cutting-options</span>
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2061
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<td class="new_line diff-line-num" data-linenumber="2129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2129
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<pre style="margin: 0;"> <span id="LC2129" class="line" lang="plaintext">Restriction site cutting options:</span>
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2062
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2130
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<pre style="margin: 0;"> <span id="LC2130" class="line" lang="plaintext">.RS</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3233,9 +3301,10 @@ Userfields (fields accepted by the \-\-userfields option):</td>
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3233
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3301
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<pre style="margin: 0;"> <span id="LC3301" class="line" lang="plaintext">.RS</span>
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<td class="old_line diff-line-num" data-linenumber="3234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3234
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3302
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<pre style="margin: 0;"> <span id="LC3302" class="line" lang="plaintext">.TP 9</span>
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3235
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3303
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<pre style="margin: 0;"> <span id="LC3303" class="line" lang="plaintext">.B aln</span>
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<td class="old_line diff-line-num old" data-linenumber="3236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3236
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<td class="new_line diff-line-num old" data-linenumber="3304" style="width: 35px; color: rgba(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="LC3236" class="line" lang="plaintext">Print a string of M (match), D (delete, i.e. a gap in the query) and I</span>
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<td class="old_line diff-line-num old" data-linenumber="3237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3237
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<td class="new_line diff-line-num old" data-linenumber="3304" style="width: 35px; color: rgba(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="LC3237" class="line" lang="plaintext">(insert, i.e. a gap in the target) representing the pairwise</span>
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<td class="old_line diff-line-num old" data-linenumber="3238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3238
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<pre style="margin: 0;">-<span id="LC3238" class="line" lang="plaintext">alignment. Empty field if there is no alignment.</span>
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3304
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<pre style="margin: 0;">+<span id="LC3304" class="line" lang="plaintext">Print a string of M (match/mismatch, i.e. not a gap), D (delete,</span>
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3305
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<pre style="margin: 0;">+<span id="LC3305" class="line" lang="plaintext">i.e. a gap in the query) and I (insert, i.e. a gap in the target)</span>
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3306
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<pre style="margin: 0;">+<span id="LC3306" class="line" lang="plaintext">representing the pairwise alignment. Empty field if there is no</span>
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3307
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<pre style="margin: 0;">+<span id="LC3307" class="line" lang="plaintext">alignment.</span>
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3239
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3308
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<pre style="margin: 0;"> <span id="LC3308" class="line" lang="plaintext">.TP</span>
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3240
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3309
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<pre style="margin: 0;"> <span id="LC3309" class="line" lang="plaintext">.B alnlen</span>
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3241
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3310
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<pre style="margin: 0;"> <span id="LC3310" class="line" lang="plaintext">Print the length of the query-target alignment (number of</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4307,6 +4376,18 @@ changes. Compiles successfully on macOS running on Apple Silicon</td>
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4307
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4376
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<pre style="margin: 0;"> <span id="LC4376" class="line" lang="plaintext">adaptations for Windows compatibility, including the use of the C++</span>
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4308
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4377
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<pre style="margin: 0;"> <span id="LC4377" class="line" lang="plaintext">standard library for regular expressions. Minor changes for</span>
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4309
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4378
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<pre style="margin: 0;"> <span id="LC4378" class="line" lang="plaintext">compatibility with Power8. Switch to C++ header files.</span>
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4379
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<pre style="margin: 0;">+<span id="LC4379" class="line" lang="plaintext">.TP</span>
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4380
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<pre style="margin: 0;">+<span id="LC4380" class="line" lang="plaintext">.BR v2.16.0\~ "released March 22nd, 2021"</span>
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4381
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<pre style="margin: 0;">+<span id="LC4381" class="line" lang="plaintext">This version adds the orient command. It also handles empty input</span>
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4382
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<pre style="margin: 0;">+<span id="LC4382" class="line" lang="plaintext">files properly. Documentation has been updated.</span>
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4383
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<pre style="margin: 0;">+<span id="LC4383" class="line" lang="plaintext">.TP</span>
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4384
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<pre style="margin: 0;">+<span id="LC4384" class="line" lang="plaintext">.BR v2.17.0\~ "released March 29nd, 2021"</span>
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4385
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<pre style="margin: 0;">+<span id="LC4385" class="line" lang="plaintext">The fastq_mergepairs command has been changed. It now allows merging</span>
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4386
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<pre style="margin: 0;">+<span id="LC4386" class="line" lang="plaintext">of sequences with overlaps as short as 5 bp if the \-\-fastq_minovlen</span>
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4387
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<pre style="margin: 0;">+<span id="LC4387" class="line" lang="plaintext">option has been adjusted down from the default 10. In addition, much</span>
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4388
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<pre style="margin: 0;">+<span id="LC4388" class="line" lang="plaintext">fewer pairs of reads should now be rejected with the reason 'multiple</span>
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4389
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<pre style="margin: 0;">+<span id="LC4389" class="line" lang="plaintext">potential alignments' as the algorithm for detecting those have been</span>
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4390
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<pre style="margin: 0;">+<span id="LC4390" class="line" lang="plaintext">changed.</span>
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4310
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4391
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<pre style="margin: 0;"> <span id="LC4391" class="line" lang="plaintext">.LP</span>
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4311
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4392
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<pre style="margin: 0;"> <span id="LC4392" class="line" lang="plaintext">.\" ============================================================================</span>
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4312
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4393
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<pre style="margin: 0;"> <span id="LC4393" class="line" lang="plaintext">.\" TODO:</span>
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<li id="67e794015a01b8816bd16290e5f8538236da8245">
<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#67e794015a01b8816bd16290e5f8538236da8245"><strong>src/Makefile.am</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">@@ -48,6 +48,7 @@ md5.h \</td>
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48
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="make">mergepairs.h <span class="se" style="color: #d14;">\</span></span>
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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="make">minheap.h <span class="se" style="color: #d14;">\</span></span>
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50
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="make">msa.h <span class="se" style="color: #d14;">\</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="make">orient.h <span class="se" style="color: #d14;">\</span></span>
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51
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="make">otutable.h <span class="se" style="color: #d14;">\</span></span>
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52
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="make">rerep.h <span class="se" style="color: #d14;">\</span></span>
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53
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="make">results.h <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -140,6 +141,7 @@ md5.c \</td>
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140
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="make">mergepairs.cc <span class="se" style="color: #d14;">\</span></span>
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141
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="make">minheap.cc <span class="se" style="color: #d14;">\</span></span>
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142
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="make">msa.cc <span class="se" style="color: #d14;">\</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#851b053a0662a1beacb7e7b0df773bc30f98c900"><strong>src/allpairs.cc</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">@@ -629,13 +629,21 @@ void allpairs_global(char * cmdline, char * progheader)</td>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_done</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt_quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching query sequences: %d of %d (%.2f%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching query sequences: %d of %d"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_log</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching query sequences: %d of %d (%.2f%%)</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching query sequences: %d of %d"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="cpp"> <span class="n" style="color: #333;">xpthread_mutex_destroy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mutex_output</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#55c7453623853a1b38dbd49f5dc20389cd203fe0"><strong>src/chimera.cc</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">@@ -1590,26 +1590,59 @@ void chimera()</td>
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<pre style="margin: 0;"> <span id="LC1590" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_done</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC1591" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1592" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt_quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1593" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1594" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Found %d (%.1f%%) chimeras, %d (%.1f%%) non-chimeras,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC1595" class="line" lang="cpp"> <span class="s" style="color: #d14;">"and %d (%.1f%%) borderline sequences in %u unique sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC1596" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Taking abundance information into account, this corresponds to</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC1597" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" (%.1f%%) chimeras, %"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" (%.1f%%) non-chimeras,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC1598" class="line" lang="cpp"> <span class="s" style="color: #d14;">"and %"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" (%.1f%%) borderline sequences in %"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" total sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1599" class="line" lang="cpp"> <span class="n" style="color: #333;">chimera_count</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1600" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chimera_count</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_count</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1601" class="line" lang="cpp"> <span class="n" style="color: #333;">nonchimera_count</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1602" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nonchimera_count</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_count</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1603" class="line" lang="cpp"> <span class="n" style="color: #333;">borderline_count</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1604" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">borderline_count</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_count</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1605" class="line" lang="cpp"> <span class="n" style="color: #333;">total_count</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1606" class="line" lang="cpp"> <span class="n" style="color: #333;">chimera_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1607" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chimera_abundance</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1608" class="line" lang="cpp"> <span class="n" style="color: #333;">nonchimera_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1609" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nonchimera_abundance</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1610" class="line" lang="cpp"> <span class="n" style="color: #333;">borderline_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1611" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">borderline_abundance</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1612" class="line" lang="cpp"> <span class="n" style="color: #333;">total_abundance</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1593" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1594" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">total_count</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1595" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1596" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Found %d (%.1f%%) chimeras, "</span></span>
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1597
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<pre style="margin: 0;">+<span id="LC1597" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%d (%.1f%%) non-chimeras,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1598
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<pre style="margin: 0;">+<span id="LC1598" class="line" lang="cpp"> <span class="s" style="color: #d14;">"and %d (%.1f%%) borderline sequences "</span></span>
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1599
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<pre style="margin: 0;">+<span id="LC1599" class="line" lang="cpp"> <span class="s" style="color: #d14;">"in %u unique sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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1600
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<pre style="margin: 0;">+<span id="LC1600" class="line" lang="cpp"> <span class="n" style="color: #333;">chimera_count</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1601" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chimera_count</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_count</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1602" class="line" lang="cpp"> <span class="n" style="color: #333;">nonchimera_count</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1603" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nonchimera_count</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_count</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1604" class="line" lang="cpp"> <span class="n" style="color: #333;">borderline_count</span><span class="p">,</span></span>
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1605
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<pre style="margin: 0;">+<span id="LC1605" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">borderline_count</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_count</span><span class="p">,</span></span>
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1606
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<pre style="margin: 0;">+<span id="LC1606" class="line" lang="cpp"> <span class="n" style="color: #333;">total_count</span><span class="p">);</span></span>
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1607
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<pre style="margin: 0;">+<span id="LC1607" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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1608
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<pre style="margin: 0;">+<span id="LC1608" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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1609
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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Found %d chimeras, "</span></span>
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1610
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<pre style="margin: 0;">+<span id="LC1610" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%d non-chimeras,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1611
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<pre style="margin: 0;">+<span id="LC1611" class="line" lang="cpp"> <span class="s" style="color: #d14;">"and %d borderline sequences "</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1612
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<pre style="margin: 0;">+<span id="LC1612" class="line" lang="cpp"> <span class="s" style="color: #d14;">"in %u unique sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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1613
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<pre style="margin: 0;">+<span id="LC1613" class="line" lang="cpp"> <span class="n" style="color: #333;">chimera_count</span><span class="p">,</span></span>
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1614
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<pre style="margin: 0;">+<span id="LC1614" class="line" lang="cpp"> <span class="n" style="color: #333;">nonchimera_count</span><span class="p">,</span></span>
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1615
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<pre style="margin: 0;">+<span id="LC1615" class="line" lang="cpp"> <span class="n" style="color: #333;">borderline_count</span><span class="p">,</span></span>
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1616
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<pre style="margin: 0;">+<span id="LC1616" class="line" lang="cpp"> <span class="n" style="color: #333;">total_count</span><span class="p">);</span></span>
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1617
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<pre style="margin: 0;">+<span id="LC1617" class="line" lang="cpp"></span>
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1618
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<pre style="margin: 0;">+<span id="LC1618" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">total_abundance</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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1619
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<pre style="margin: 0;">+<span id="LC1619" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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1620
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<pre style="margin: 0;">+<span id="LC1620" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Taking abundance information into account, "</span></span>
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1621
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<pre style="margin: 0;">+<span id="LC1621" class="line" lang="cpp"> <span class="s" style="color: #d14;">"this corresponds to</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1622
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<pre style="margin: 0;">+<span id="LC1622" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" (%.1f%%) chimeras, "</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1623
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<pre style="margin: 0;">+<span id="LC1623" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" (%.1f%%) non-chimeras,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1624
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<pre style="margin: 0;">+<span id="LC1624" class="line" lang="cpp"> <span class="s" style="color: #d14;">"and %"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" (%.1f%%) borderline sequences "</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1625
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<pre style="margin: 0;">+<span id="LC1625" class="line" lang="cpp"> <span class="s" style="color: #d14;">"in %"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" total sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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1626
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<pre style="margin: 0;">+<span id="LC1626" class="line" lang="cpp"> <span class="n" style="color: #333;">chimera_abundance</span><span class="p">,</span></span>
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1627
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<pre style="margin: 0;">+<span id="LC1627" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chimera_abundance</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1628" class="line" lang="cpp"> <span class="n" style="color: #333;">nonchimera_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1629" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nonchimera_abundance</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_abundance</span><span class="p">,</span></span>
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1630
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<pre style="margin: 0;">+<span id="LC1630" class="line" lang="cpp"> <span class="n" style="color: #333;">borderline_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1631" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">borderline_abundance</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1632" class="line" lang="cpp"> <span class="n" style="color: #333;">total_abundance</span><span class="p">);</span></span>
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1633
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<pre style="margin: 0;">+<span id="LC1633" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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1634
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<pre style="margin: 0;">+<span id="LC1634" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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1635
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<pre style="margin: 0;">+<span id="LC1635" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Taking abundance information into account, "</span></span>
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1636
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<pre style="margin: 0;">+<span id="LC1636" class="line" lang="cpp"> <span class="s" style="color: #d14;">"this corresponds to</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1637
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<pre style="margin: 0;">+<span id="LC1637" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" chimeras, "</span></span>
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1638
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<pre style="margin: 0;">+<span id="LC1638" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" non-chimeras,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1639
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<pre style="margin: 0;">+<span id="LC1639" class="line" lang="cpp"> <span class="s" style="color: #d14;">"and %"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" borderline sequences "</span></span>
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1640
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<pre style="margin: 0;">+<span id="LC1640" class="line" lang="cpp"> <span class="s" style="color: #d14;">"in %"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" total sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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1641
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<pre style="margin: 0;">+<span id="LC1641" class="line" lang="cpp"> <span class="n" style="color: #333;">chimera_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1642" class="line" lang="cpp"> <span class="n" style="color: #333;">nonchimera_abundance</span><span class="p">,</span></span>
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1643
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<pre style="margin: 0;">+<span id="LC1643" class="line" lang="cpp"> <span class="n" style="color: #333;">borderline_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1644" class="line" lang="cpp"> <span class="n" style="color: #333;">total_abundance</span><span class="p">);</span></span>
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1645
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<pre style="margin: 0;">+<span id="LC1645" class="line" lang="cpp"> <span class="p">}</span></span>
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1646
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<pre style="margin: 0;"> <span id="LC1646" class="line" lang="cpp"></span>
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1647
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<pre style="margin: 0;"> <span id="LC1647" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_log</span><span class="p">)</span></span>
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1648
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<pre style="margin: 0;"> <span id="LC1648" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1617,10 +1650,16 @@ void chimera()</td>
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<pre style="margin: 0;"> <span id="LC1650" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">opt_uchime_ref</span><span class="p">);</span></span>
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1618
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1651
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<pre style="margin: 0;"> <span id="LC1651" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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1652
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<pre style="margin: 0;"> <span id="LC1652" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">denovo_dbname</span><span class="p">);</span></span>
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1620
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<pre style="margin: 0;">-<span id="LC1620" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">": %d/%u chimeras (%.1f%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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1621
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<pre style="margin: 0;">-<span id="LC1621" class="line" lang="cpp"> <span class="n" style="color: #333;">chimera_count</span><span class="p">,</span></span>
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1622
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<pre style="margin: 0;">-<span id="LC1622" class="line" lang="cpp"> <span class="n" style="color: #333;">seqno</span><span class="p">,</span></span>
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1623
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<pre style="margin: 0;">-<span id="LC1623" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chimera_count</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">seqno</span><span class="p">);</span></span>
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1653
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<pre style="margin: 0;">+<span id="LC1653" class="line" lang="cpp"></span>
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1654
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<pre style="margin: 0;">+<span id="LC1654" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seqno</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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1655
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<pre style="margin: 0;">+<span id="LC1655" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">": %d/%u chimeras (%.1f%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1656" class="line" lang="cpp"> <span class="n" style="color: #333;">chimera_count</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1657" class="line" lang="cpp"> <span class="n" style="color: #333;">seqno</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1658" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chimera_count</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">seqno</span><span class="p">);</span></span>
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1659
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<pre style="margin: 0;">+<span id="LC1659" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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1660
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<pre style="margin: 0;">+<span id="LC1660" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">": %d/%u chimeras</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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1661
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<pre style="margin: 0;">+<span id="LC1661" class="line" lang="cpp"> <span class="n" style="color: #333;">chimera_count</span><span class="p">,</span></span>
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1662
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<pre style="margin: 0;">+<span id="LC1662" class="line" lang="cpp"> <span class="n" style="color: #333;">seqno</span><span class="p">);</span></span>
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1663
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<pre style="margin: 0;"> <span id="LC1663" class="line" lang="cpp"> <span class="p">}</span></span>
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1664
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<pre style="margin: 0;"> <span id="LC1664" class="line" lang="cpp"></span>
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1665
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#f39ff334aa80788f730c6c2fa78e9dda01843d21"><strong>src/eestats.cc</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">@@ -482,8 +482,14 @@ void fastq_eestats2()</td>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_done</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_output</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" reads, max len %"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">", avg %.1f</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="cpp"> <span class="n" style="color: #333;">seq_count</span><span class="p">,</span> <span class="n" style="color: #333;">longest</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">symbols</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">seq_count</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" reads"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"> <span class="n" style="color: #333;">seq_count</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq_count</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_output</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp"> <span class="s" style="color: #d14;">", max len %"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">", avg %.1f"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"> <span class="n" style="color: #333;">longest</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">symbols</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">seq_count</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_output</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_output</span><span class="p">,</span> <span class="s" style="color: #d14;">"Length"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">opt_ee_cutoffs_count</span><span class="p">;</span> <span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,7 +64,7 @@ fastx_handle fasta_open(const char * filename)</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">fastx_handle</span> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastx_open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastx_is_fastq</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastx_is_fastq</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">h</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">is_empty</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"FASTA file expected, FASTQ file found (%s)"</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">h</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#da9831bd375e4011e4dc95b4edb9ec2b35d91bb0"><strong>src/fastqjoin.cc</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">@@ -238,8 +238,10 @@ void fastq_join()</td>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="n" style="color: #333;">fastq_close</span><span class="p">(</span><span class="n" style="color: #333;">fastq_fwd</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"> <span class="n" style="color: #333;">fastq_fwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">qual</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qual</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">qual</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">padgap</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">padgapq</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#6f963d02896322eab19500836bca3f9a22619a35"><strong>src/fastqops.cc</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">@@ -185,66 +185,69 @@ void fastq_chars()</td>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Read %"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">seq_count</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Qmin %d, QMax %d, Range %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">qmin</span><span class="p">,</span> <span class="n" style="color: #333;">qmax</span><span class="p">,</span> <span class="n" style="color: #333;">qmax</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">qmin</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq_count</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"> <span class="p">{</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Qmin %d, QMax %d, Range %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"> <span class="n" style="color: #333;">qmin</span><span class="p">,</span> <span class="n" style="color: #333;">qmax</span><span class="p">,</span> <span class="n" style="color: #333;">qmax</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">qmin</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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190
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: -fastq_qmin %d -fastq_qmax %d -fastq_ascii %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">fastq_qmin</span><span class="p">,</span> <span class="n" style="color: #333;">fastq_qmax</span><span class="p">,</span> <span class="n" style="color: #333;">fastq_ascii</span><span class="p">);</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: -fastq_qmin %d -fastq_qmax %d -fastq_ascii %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fastq_qmin</span><span class="p">,</span> <span class="n" style="color: #333;">fastq_qmax</span><span class="p">,</span> <span class="n" style="color: #333;">fastq_ascii</span><span class="p">);</span></span>
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193
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastq_ascii</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="cpp"> <span class="p">{</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmin</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Solexa format (phred+64)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmin</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">66</span><span class="p">)</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Illumina 1.3+ format (phred+64)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Illumina 1.5+ format (phred+64)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="cpp"> <span class="p">}</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="cpp"> <span class="p">{</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmax</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">73</span><span class="p">)</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Illumina 1.8+ format (phred+33)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastq_ascii</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="p">{</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmin</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Solexa format (phred+64)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmin</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">66</span><span class="p">)</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Illumina 1.3+ format (phred+64)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Illumina 1.5+ format (phred+64)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="p">}</span></span>
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207
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Original Sanger format (phred+33)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="cpp"> <span class="p">}</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="p">{</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmax</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">73</span><span class="p">)</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Illumina 1.8+ format (phred+33)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Original Sanger format (phred+33)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="p">}</span></span>
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210
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Letter N Freq MaxRun</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"------ ---------- ------ ------</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Letter N Freq MaxRun</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"------ ---------- ------ ------</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">256</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp"> <span class="p">{</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequence_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">256</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" %c %10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" %5.1f%% %6d"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">sequence_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">],</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sequence_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_chars</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">maxrun</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">))</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequence_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmin_n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">qmax_n</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" Q=%c..%c"</span><span class="p">,</span> <span class="n" style="color: #333;">qmin_n</span><span class="p">,</span> <span class="n" style="color: #333;">qmax_n</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" Q=%c"</span><span class="p">,</span> <span class="n" style="color: #333;">qmin_n</span><span class="p">);</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" %c %10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" %5.1f%% %6d"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">sequence_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sequence_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_chars</span><span class="p">,</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">maxrun</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]);</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"> <span class="p">{</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmin_n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">qmax_n</span><span class="p">)</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" Q=%c..%c"</span><span class="p">,</span> <span class="n" style="color: #333;">qmin_n</span><span class="p">,</span> <span class="n" style="color: #333;">qmax_n</span><span class="p">);</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" Q=%c"</span><span class="p">,</span> <span class="n" style="color: #333;">qmin_n</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Char ASCII Freq Tails</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"---- ----- ------ ----------</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Char ASCII Freq Tails</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"---- ----- ------ ----------</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qmin</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">qmax</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">quality_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qmin</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">qmax</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" '%c' %5d %5.1f%% %10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">quality_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_chars</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp"> <span class="n" style="color: #333;">tail_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">quality_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" '%c' %5d %5.1f%% %10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">quality_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_chars</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">tail_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -253,66 +256,69 @@ void fastq_chars()</td>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="p">{</span></span>
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Read %"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">seq_count</span><span class="p">);</span></span>
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Qmin %d, QMax %d, Range %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp"> <span class="n" style="color: #333;">qmin</span><span class="p">,</span> <span class="n" style="color: #333;">qmax</span><span class="p">,</span> <span class="n" style="color: #333;">qmax</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">qmin</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq_count</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Qmin %d, QMax %d, Range %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;">qmin</span><span class="p">,</span> <span class="n" style="color: #333;">qmax</span><span class="p">,</span> <span class="n" style="color: #333;">qmax</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">qmin</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: -fastq_qmin %d -fastq_qmax %d -fastq_ascii %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cpp"> <span class="n" style="color: #333;">fastq_qmin</span><span class="p">,</span> <span class="n" style="color: #333;">fastq_qmax</span><span class="p">,</span> <span class="n" style="color: #333;">fastq_ascii</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: -fastq_qmin %d -fastq_qmax %d -fastq_ascii %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fastq_qmin</span><span class="p">,</span> <span class="n" style="color: #333;">fastq_qmax</span><span class="p">,</span> <span class="n" style="color: #333;">fastq_ascii</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastq_ascii</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmin</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Solexa format (phred+64)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmin</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">66</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Illumina 1.3+ format (phred+64)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Illumina 1.5+ format (phred+64)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmax</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">73</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Illumina 1.8+ format (phred+33)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastq_ascii</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"> <span class="p">{</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmin</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Solexa format (phred+64)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmin</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">66</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Illumina 1.3+ format (phred+64)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Illumina 1.5+ format (phred+64)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Original Sanger format (phred+33)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp"> <span class="p">}</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="p">{</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmax</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">73</span><span class="p">)</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Illumina 1.8+ format (phred+33)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Guess: Original Sanger format (phred+33)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="p">}</span></span>
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278
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Letter N Freq MaxRun</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"------ ---------- ------ ------</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Letter N Freq MaxRun</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"------ ---------- ------ ------</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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282
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">256</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="cpp"> <span class="p">{</span></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequence_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">256</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" %c %10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" %5.1f%% %6d"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">sequence_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sequence_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_chars</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cpp"> <span class="n" style="color: #333;">maxrun</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequence_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmin_n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">qmax_n</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" Q=%c..%c"</span><span class="p">,</span> <span class="n" style="color: #333;">qmin_n</span><span class="p">,</span> <span class="n" style="color: #333;">qmax_n</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" Q=%c"</span><span class="p">,</span> <span class="n" style="color: #333;">qmin_n</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" %c %10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" %5.1f%% %6d"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">sequence_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sequence_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_chars</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">maxrun</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qmin_n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">qmax_n</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" Q=%c..%c"</span><span class="p">,</span> <span class="n" style="color: #333;">qmin_n</span><span class="p">,</span> <span class="n" style="color: #333;">qmax_n</span><span class="p">);</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" Q=%c"</span><span class="p">,</span> <span class="n" style="color: #333;">qmin_n</span><span class="p">);</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="p">}</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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298
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp"> <span class="p">}</span></span>
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299
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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300
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp"> <span class="p">}</span></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="cpp"> <span class="p">}</span></span>
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302
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Char ASCII Freq Tails</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"---- ----- ------ ----------</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Char ASCII Freq Tails</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"---- ----- ------ ----------</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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306
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qmin</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">qmax</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cpp"> <span class="p">{</span></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">quality_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qmin</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">qmax</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" '%c' %5d %5.1f%% %10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">quality_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_chars</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cpp"> <span class="n" style="color: #333;">tail_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">quality_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" '%c' %5d %5.1f%% %10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">quality_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_chars</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">tail_chars</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="622" style="width: 35px; color: rgba(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">@@ -622,7 +628,8 @@ void fastq_stats()</td>
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628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"%10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" Recs (%.1lfM), 0 too long</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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630
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="cpp"> <span class="n" style="color: #333;">seq_count</span><span class="p">,</span> <span class="n" style="color: #333;">seq_count</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">1.0e6</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"%10.1lf Avg length</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">symbols</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">seq_count</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq_count</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"%10.1lf Avg length</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">symbols</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">seq_count</span><span class="p">);</span></span>
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633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"%9.1lfM Bases</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">symbols</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">1.0e6</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="cpp"> <span class="p">}</span></span>
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635
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -658,7 +665,7 @@ void fastx_revcomp()</td>
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665
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">h</span><span class="p">)</span></span>
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666
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized file type (not proper FASTA or FASTQ format)"</span><span class="p">);</span></span>
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667
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"></span>
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661
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastqout</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span><span class="p">)</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastqout</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">h</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">is_empty</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot write FASTQ output with a FASTA input file, lacking quality scores"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">filesize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastx_get_size</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">);</span></span>
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<li id="66934cf2fb3d65e60500632c125c6324b6bebbec">
<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#66934cf2fb3d65e60500632c125c6324b6bebbec"><strong>src/fastx.cc</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">@@ -275,13 +275,20 @@ fastx_handle fastx_open(const char * filename)</td>
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">magic</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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276
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"></span>
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277
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FORMAT_PLAIN</span><span class="p">;</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">magic</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to read from file (%s)"</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">magic</span><span class="p">,</span> <span class="n" style="color: #333;">MAGIC_GZIP</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FORMAT_GZIP</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">magic</span><span class="p">,</span> <span class="n" style="color: #333;">MAGIC_BZIP</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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284
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<td class="new_line diff-line-num old" data-linenumber="279" style="width: 35px; color: rgba(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="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FORMAT_BZIP</span><span class="p">;</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bytes_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">magic</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bytes_read</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="p">{</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">magic</span><span class="p">,</span> <span class="n" style="color: #333;">MAGIC_GZIP</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FORMAT_GZIP</span><span class="p">;</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">magic</span><span class="p">,</span> <span class="n" style="color: #333;">MAGIC_BZIP</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FORMAT_BZIP</span><span class="p">;</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="p">}</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="p">{</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* consider it an empty file or a tiny fasta file, uncompressed */</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="p">}</span></span>
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"></span>
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286
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* close and reopen to avoid problems with gzip library */</span></span>
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287
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* rewind was not enough */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -330,65 +337,71 @@ fastx_handle fastx_open(const char * filename)</td>
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330
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337
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastx_file_fill_buffer</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"File too small"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* examine first char and see if it starts with > or @ */</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">filetype</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">file_buffer</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_empty</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">filetype</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'@'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">filetype</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_empty</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filetype</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* close files if unrecognized file type */</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">file_buffer</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">switch</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">h</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">format</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">first</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><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="LC353" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FORMAT_PLAIN</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="n" style="color: #333;">filetype</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'@'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="n" style="color: #333;">filetype</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"></span>
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362
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FORMAT_GZIP</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filetype</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="p">{</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* close files if unrecognized file type */</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">format</span><span class="p">)</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FORMAT_PLAIN</span><span class="p">:</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FORMAT_GZIP</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_ZLIB_H</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gzclose_p</span><span class="p">)(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_gz</span><span class="p">);</span></span>
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365
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_gz</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gzclose_p</span><span class="p">)(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_gz</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_gz</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC376" 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="LC377" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FORMAT_BZIP</span><span class="p">:</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FORMAT_BZIP</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_BZLIB_H</span></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">BZ2_bzReadClose_p</span><span class="p">)(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bzError</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bz</span><span class="p">);</span></span>
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372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bz</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">BZ2_bzReadClose_p</span><span class="p">)(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bzError</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bz</span><span class="p">);</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bz</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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374
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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375
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp"></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="cpp"> <span class="nl">default:</span></span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Internal error"</span><span class="p">);</span></span>
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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="cpp"> <span class="p">}</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="nl">default:</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Internal error"</span><span class="p">);</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="p">}</span></span>
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379
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp</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="idiff left right"> </span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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382
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp"></span>
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383
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<td class="new_line diff-line-num old" data-linenumber="392" style="width: 35px; color: rgba(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="LC383" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">MAGIC_GZIP</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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384
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<td class="new_line diff-line-num old" data-linenumber="392" style="width: 35px; color: rgba(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="LC384" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"File appears to be gzip compressed. Please use --gzip_decompress"</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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">2</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="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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">MAGIC_GZIP</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"File appears to be gzip compressed. Please use --gzip_decompress"</span><span class="p">);</span></span>
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385
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp"></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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">MAGIC_BZIP</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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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;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"File appears to be bzip2 compressed. Please use --bzip2_decompress"</span><span class="p">);</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">MAGIC_BZIP</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"File appears to be bzip2 compressed. Please use --bzip2_decompress"</span><span class="p">);</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"> <span class="p">}</span></span>
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388
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cpp"></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"File type not recognized."</span><span class="p">);</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"File type not recognized."</span><span class="p">);</span></span>
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp"></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;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="p">}</span></span>
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"> <span class="p">}</span></span>
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"></span>
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* more initialization */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -412,7 +425,7 @@ fastx_handle fastx_open(const char * filename)</td>
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412
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp"></span>
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413
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426
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">fastx_is_fastq</span><span class="p">(</span><span class="n" style="color: #333;">fastx_handle</span> <span class="n" style="color: #333;">h</span><span class="p">)</span></span>
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414
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427
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cpp"><span class="p">{</span></span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">h</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">is_empty</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"><span class="p">}</span></span>
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp"></span>
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431
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">fastx_close</span><span class="p">(</span><span class="n" style="color: #333;">fastx_handle</span> <span class="n" style="color: #333;">h</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -426,6 +439,7 @@ void fastx_close(fastx_handle h)</td>
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439
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripped</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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440
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" %c(%"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">")"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripped</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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441
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"REMINDER: vsearch does not support amino acid sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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443
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_log</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -434,6 +448,7 @@ void fastx_close(fastx_handle h)</td>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripped</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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449
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" %c(%"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">")"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stripped</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"REMINDER: vsearch does not support amino acid sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -661,4 +676,3 @@ int64_t fastx_get_abundance(fastx_handle h)</td>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fasta_get_abundance</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">);</span></span>
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678
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="cpp"></span></pre>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#10eff3279cfc990f0a974eabcc8aa2d695e029f5"><strong>src/fastx.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -77,6 +77,7 @@ struct fastx_s</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">is_pipe</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">is_fastq</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">is_empty</span><span class="p">;</span></span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp</span><span class="p">;</span></span>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#5158e97b06e3c2eb531bf6a179b392990120db5a"><strong>src/filter.cc</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">@@ -223,7 +223,7 @@ void filter(bool fastq_only, char * filename)</td>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">h1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized file type (not proper FASTA or FASTQ format)"</span><span class="p">);</span></span>
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">h1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">h1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">h1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">is_empty</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastq_only</span><span class="p">)</span></span>
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -259,7 +259,7 @@ void filter(bool fastq_only, char * filename)</td>
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259
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">h1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">h2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span><span class="p">)</span></span>
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"The forward and reverse input sequence must in the same format, either FASTA or FASTQ"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">h2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">h2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">h2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">is_empty</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastq_only</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"> <span class="p">{</span></span>
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<li id="f8033b5b738e4f851faa382f3ee8786c9fbd889d">
<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#f8033b5b738e4f851faa382f3ee8786c9fbd889d"><strong>src/getseq.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -318,7 +318,7 @@ void getseq(char * filename)</td>
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318
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">h1</span><span class="p">)</span></span>
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319
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized file type (not proper FASTA or FASTQ format)"</span><span class="p">);</span></span>
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">opt_fastqout</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_notmatchedfq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">h1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">opt_fastqout</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_notmatchedfq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">h1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_fastq</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">h1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">is_empty</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot write FASTQ output from FASTA input"</span><span class="p">);</span></span>
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">filesize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastx_get_size</span><span class="p">(</span><span class="n" style="color: #333;">h1</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="448" style="width: 35px; color: rgba(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">@@ -448,18 +448,30 @@ void getseq(char * filename)</td>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_done</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">opt_quiet</span><span class="p">)</span></span>
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451
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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452
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" of %"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" sequences extracted (%.1lf%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">kept</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="cpp"> <span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">discarded</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">discarded</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" of %"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" sequences extracted"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"> <span class="n" style="color: #333;">kept</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"> <span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">discarded</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">discarded</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp"> <span class="s" style="color: #d14;">" (%.1lf%%)"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">discarded</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_log</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" of %"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" sequences extracted (%.1lf%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="cpp"> <span class="n" style="color: #333;">kept</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="cpp"> <span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">discarded</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">discarded</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" of %"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">" sequences extracted"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cpp"> <span class="n" style="color: #333;">kept</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"> <span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">discarded</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">discarded</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"> <span class="s" style="color: #d14;">" (%.1lf%%)"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">kept</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">discarded</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastaout</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp_fastaout</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#9c689a31237f70b17e9bac31f42d1b22ea1d59be"><strong>src/mergepairs.cc</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">@@ -68,10 +68,9 @@ static const int chunk_factor = 2; /* chunks per thread */</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* scores in bits */</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">merge_minscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">16.0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">merge_mindiagcount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">merge_minscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">16.0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">merge_dropmax</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">16.0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">merge_mindiagcount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">merge_minrepeatdiagcount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">12</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">merge_mismatchmax</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">4.0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* static variables */</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -686,13 +685,6 @@ int64_t optimize(merge_data_t * ip,</td>
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="cpp"> <span class="n" style="color: #333;">kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">diagcount</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">merge_minrepeatdiagcount</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="cpp"> <span class="n" style="color: #333;">hits</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hits</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* for each interesting diagonal */</span></span>
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">fwd_3prime_overhang</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -747,6 +739,9 @@ int64_t optimize(merge_data_t * ip,</td>
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dropmax</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">merge_dropmax</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="cpp"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">merge_minscore</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="cpp"> <span class="n" style="color: #333;">hits</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">best_score</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="cpp"> <span class="n" style="color: #333;">best_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1280,6 +1275,18 @@ void pair_all()</td>
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<pre style="margin: 0;"> <span id="LC1275" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1276" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">fastq_mergepairs</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC1277" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* fatal error if specified overlap is too small */</span></span>
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1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastq_minovlen</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Overlap specified with --fastq_minovlen must be at least 5"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* relax default parameters in case of short overlaps */</span></span>
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastq_minovlen</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">9</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="cpp"> <span class="n" style="color: #333;">merge_mindiagcount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_fastq_minovlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="cpp"> <span class="n" style="color: #333;">merge_minscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.6</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_fastq_minovlen</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1290" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1291" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* open input files */</span></span>
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<pre style="margin: 0;"> <span id="LC1292" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1312,7 +1319,8 @@ void fastq_mergepairs()</td>
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1312
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1319
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<pre style="margin: 0;"> <span id="LC1319" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">filesize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastq_get_size</span><span class="p">(</span><span class="n" style="color: #333;">fastq_fwd</span><span class="p">);</span></span>
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1313
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1320
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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_init</span><span class="p">(</span><span class="s" style="color: #d14;">"Merging reads"</span><span class="p">,</span> <span class="n" style="color: #333;">filesize</span><span class="p">);</span></span>
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1314
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1321
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="cpp"></span>
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1315
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<pre style="margin: 0;">-<span id="LC1315" class="line" lang="cpp"> <span class="n" style="color: #333;">pair_all</span><span class="p">();</span></span>
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1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">fastq_fwd</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_empty</span><span class="p">)</span></span>
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1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="cpp"> <span class="n" style="color: #333;">pair_all</span><span class="p">();</span></span>
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1316
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1324
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="cpp"></span>
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1317
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1325
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<pre style="margin: 0;"> <span id="LC1325" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_done</span><span class="p">();</span></span>
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1318
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1326
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<pre style="margin: 0;"> <span id="LC1326" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1324,14 +1332,22 @@ void fastq_mergepairs()</td>
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1324
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1332
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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="cpp"> <span class="n" style="color: #333;">total</span><span class="p">);</span></span>
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1325
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1333
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<pre style="margin: 0;"> <span id="LC1333" class="line" lang="cpp"></span>
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1326
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1334
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<pre style="margin: 0;"> <span id="LC1334" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1327
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<td class="new_line diff-line-num old" data-linenumber="1335" style="width: 35px; color: rgba(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="LC1327" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" Merged (%.1lf%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1328
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<pre style="margin: 0;">-<span id="LC1328" class="line" lang="cpp"> <span class="n" style="color: #333;">merged</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1329
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<pre style="margin: 0;">-<span id="LC1329" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">merged</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total</span><span class="p">);</span></span>
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1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" Merged"</span><span class="p">,</span></span>
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1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="cpp"> <span class="n" style="color: #333;">merged</span><span class="p">);</span></span>
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1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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1338
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="cpp"> <span class="s" style="color: #d14;">" (%.1lf%%)"</span><span class="p">,</span></span>
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1340
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">merged</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total</span><span class="p">);</span></span>
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1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1332" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" Not merged (%.1lf%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1333" class="line" lang="cpp"> <span class="n" style="color: #333;">notmerged</span><span class="p">,</span></span>
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1334
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<pre style="margin: 0;">-<span id="LC1334" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">notmerged</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total</span><span class="p">);</span></span>
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1344
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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" Not merged"</span><span class="p">,</span></span>
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1345
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="cpp"> <span class="n" style="color: #333;">notmerged</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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1347
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<pre style="margin: 0;">+<span id="LC1347" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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1348
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<pre style="margin: 0;">+<span id="LC1348" class="line" lang="cpp"> <span class="s" style="color: #d14;">" (%.1lf%%)"</span><span class="p">,</span></span>
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1349
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">notmerged</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total</span><span class="p">);</span></span>
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1350
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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1351
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<pre style="margin: 0;"> <span id="LC1351" class="line" lang="cpp"></span>
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1352
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<pre style="margin: 0;"> <span id="LC1352" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">notmerged</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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1353
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<pre style="margin: 0;"> <span id="LC1353" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Pairs that failed merging due to various reasons:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1413,13 +1429,16 @@ void fastq_mergepairs()</td>
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1429
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<pre style="margin: 0;"> <span id="LC1429" class="line" lang="cpp"></span>
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1414
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1430
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<pre style="margin: 0;"> <span id="LC1430" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1415
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1431
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<pre style="margin: 0;"> <span id="LC1431" class="line" lang="cpp"></span>
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1416
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<pre style="margin: 0;">-<span id="LC1416" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Statistics of all reads:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1432
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<pre style="margin: 0;">+<span id="LC1432" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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1433
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<pre style="margin: 0;">+<span id="LC1433" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Statistics of all reads:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1435" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1418" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mean_read_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sum_read_length</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mf" style="color: #099;">2.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pairs_read</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1436" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mean_read_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sum_read_length</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mf" style="color: #099;">2.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pairs_read</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1437" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1420" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1421" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%10.2f Mean read length</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1422" class="line" lang="cpp"> <span class="n" style="color: #333;">mean_read_length</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1438" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1439" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%10.2f Mean read length</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1440" class="line" lang="cpp"> <span class="n" style="color: #333;">mean_read_length</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1441" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1442" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1443" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merged</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="cpp"> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#863c3ef39e4bd150cec0b310a7eb2384b22670a1"><strong>src/orient.cc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> VSEARCH: a versatile open source tool for metagenomics</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2014-2021, Torbjorn Rognes, Frederic Mahe and Tomas Flouri</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> All rights reserved.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Contact: Torbjorn Rognes <torognes@ifi.uio.no>,</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Department of Informatics, University of Oslo,</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> PO Box 1080 Blindern, NO-0316 Oslo, Norway</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> This software is dual-licensed and available under a choice</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> of one of two licenses, either under the terms of the GNU</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> General Public License version 3 or the BSD 2-Clause License.</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> GNU General Public License version 3</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> This program is free software: you can redistribute it and/or modify</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> it under the terms of the GNU General Public License as published by</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> the Free Software Foundation, either version 3 of the License, or</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> (at your option) any later version.</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> This program is distributed in the hope that it will be useful,</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> GNU General Public License for more details.</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> You should have received a copy of the GNU General Public License</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> The BSD 2-Clause License</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Redistribution and use in source and binary forms, with or without</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> modification, are permitted provided that the following conditions</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> are met:</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> 1. Redistributions of source code must retain the above copyright</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> notice, this list of conditions and the following disclaimer.</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> 2. Redistributions in binary form must reproduce the above copyright</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> notice, this list of conditions and the following disclaimer in the</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> POSSIBILITY OF SUCH DAMAGE.</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "vsearch.h"</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">rc_kmer</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmer</span><span class="p">)</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"><span class="p">{</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* reverse complement a kmer where k = opt_wordlength */</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmer</span><span class="p">;</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">opt_wordlength</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="p">{</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">fwd</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3U</span><span class="p">)</span> <span class="o" style="font-weight: 600;">^</span> <span class="mi" style="color: #099;">3U</span><span class="p">;</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">fwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fwd</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">2U</span><span class="p">;</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rev</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2U</span><span class="p">;</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">rev</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="p">}</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rev</span><span class="p">;</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"><span class="p">}</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">orient</span><span class="p">()</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"><span class="p">{</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">fastx_handle</span> <span class="n" style="color: #333;">query_h</span><span class="p">;</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp_fastaout</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp_fastqout</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp_tabbedout</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp_notmatched</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">matches_fwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">matches_rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">notmatched</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* check arguments */</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">opt_db</span><span class="p">)</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Database not specified with --db"</span><span class="p">);</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastaout</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_fastqout</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_notmatched</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_tabbedout</span><span class="p">))</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Output file not specified with --fastaout, --fastqout, --notmatched or --tabbedout"</span><span class="p">);</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* prepare reading of queries */</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">query_h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastx_open</span><span class="p">(</span><span class="n" style="color: #333;">opt_orient</span><span class="p">);</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* open output files */</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastaout</span><span class="p">)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">fp_fastaout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen_output</span><span class="p">(</span><span class="n" style="color: #333;">opt_fastaout</span><span class="p">);</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">fp_fastaout</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to open fasta output file for writing"</span><span class="p">);</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="p">}</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastqout</span><span class="p">)</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">fastx_is_fastq</span><span class="p">(</span><span class="n" style="color: #333;">query_h</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot write FASTQ output with FASTA input"</span><span class="p">);</span></span>
</pre>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">fp_fastqout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen_output</span><span class="p">(</span><span class="n" style="color: #333;">opt_fastqout</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">fp_fastqout</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to open fastq output file for writing"</span><span class="p">);</span></span>
</pre>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="p">}</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_notmatched</span><span class="p">)</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="p">{</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">fp_notmatched</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen_output</span><span class="p">(</span><span class="n" style="color: #333;">opt_notmatched</span><span class="p">);</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">fp_notmatched</span><span class="p">)</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to open notmatched output file for writing"</span><span class="p">);</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="p">}</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_tabbedout</span><span class="p">)</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">fp_tabbedout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen_output</span><span class="p">(</span><span class="n" style="color: #333;">opt_tabbedout</span><span class="p">);</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">fp_tabbedout</span><span class="p">)</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to open tabbedout output file for writing"</span><span class="p">);</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="p">}</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* check if it may be an UDB file */</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">is_udb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">udb_detect_isudb</span><span class="p">(</span><span class="n" style="color: #333;">opt_db</span><span class="p">);</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_udb</span><span class="p">)</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">udb_read</span><span class="p">(</span><span class="n" style="color: #333;">opt_db</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">db_read</span><span class="p">(</span><span class="n" style="color: #333;">opt_db</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">is_udb</span><span class="p">)</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="p">{</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_dbmask</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">MASK_DUST</span><span class="p">)</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">dust_all</span><span class="p">();</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">opt_dbmask</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">MASK_SOFT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">opt_hardmask</span><span class="p">))</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">hardmask_all</span><span class="p">();</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="p">}</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">is_udb</span><span class="p">)</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="p">{</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">dbindex_prepare</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">opt_dbmask</span><span class="p">);</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">dbindex_addallsequences</span><span class="p">(</span><span class="n" style="color: #333;">opt_dbmask</span><span class="p">);</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="p">}</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">uhandle_s</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">uh_fwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unique_init</span><span class="p">();</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">alloc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qseq_rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">query_qual_rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_init</span><span class="p">(</span><span class="s" style="color: #d14;">"Orienting sequences"</span><span class="p">,</span> <span class="n" style="color: #333;">fasta_get_size</span><span class="p">(</span><span class="n" style="color: #333;">query_h</span><span class="p">));</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">fastx_next</span><span class="p">(</span><span class="n" style="color: #333;">query_h</span><span class="p">,</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">opt_notrunclabels</span><span class="p">,</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="n" style="color: #333;">chrmap_no_change</span><span class="p">))</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="p">{</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">query_head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastx_get_header</span><span class="p">(</span><span class="n" style="color: #333;">query_h</span><span class="p">);</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">query_head_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastx_get_header_length</span><span class="p">(</span><span class="n" style="color: #333;">query_h</span><span class="p">);</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qseq_fwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastx_get_sequence</span><span class="p">(</span><span class="n" style="color: #333;">query_h</span><span class="p">);</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qseqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastx_get_sequence_length</span><span class="p">(</span><span class="n" style="color: #333;">query_h</span><span class="p">);</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastx_get_abundance</span><span class="p">(</span><span class="n" style="color: #333;">query_h</span><span class="p">);</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">query_qual_fwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastx_get_quality</span><span class="p">(</span><span class="n" style="color: #333;">query_h</span><span class="p">);</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* find kmers in query sequence */</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmer_count_fwd</span><span class="p">;</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmer_list_fwd</span><span class="p">;</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">unique_count</span><span class="p">(</span><span class="n" style="color: #333;">uh_fwd</span><span class="p">,</span> <span class="n" style="color: #333;">opt_wordlength</span><span class="p">,</span> <span class="n" style="color: #333;">qseqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_fwd</span><span class="p">,</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kmer_count_fwd</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kmer_list_fwd</span><span class="p">,</span> <span class="n" style="color: #333;">opt_qmask</span><span class="p">);</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* count kmers matching on each strand */</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count_fwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count_rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hits_factor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">kmer_count_fwd</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="p">{</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmer_fwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmer_list_fwd</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmer_rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rc_kmer</span><span class="p">(</span><span class="n" style="color: #333;">kmer_fwd</span><span class="p">);</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hits_fwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dbindex_getmatchcount</span><span class="p">(</span><span class="n" style="color: #333;">kmer_fwd</span><span class="p">);</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hits_rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dbindex_getmatchcount</span><span class="p">(</span><span class="n" style="color: #333;">kmer_rev</span><span class="p">);</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* require 8 times as many matches on one stand than the other */</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hits_fwd</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">hits_factor</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hits_rev</span><span class="p">)</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">count_fwd</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hits_rev</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">hits_factor</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hits_fwd</span><span class="p">)</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">count_rev</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="p">}</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* get progress as amount of input file read */</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta_get_position</span><span class="p">(</span><span class="n" style="color: #333;">query_h</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* update stats */</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;">queries</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_factor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">count_fwd</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_count</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">count_fwd</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_factor</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">count_rev</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* fwd */</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">matches_fwd</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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233
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastaout</span><span class="p">)</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">fasta_print_general</span><span class="p">(</span><span class="n" style="color: #333;">fp_fastaout</span><span class="p">,</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">qseq_fwd</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="n" style="color: #333;">qseqlen</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="n" style="color: #333;">query_head</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="n" style="color: #333;">query_head_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">qsize</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastqout</span><span class="p">)</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">fastq_print_general</span><span class="p">(</span><span class="n" style="color: #333;">fp_fastqout</span><span class="p">,</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">qseq_fwd</span><span class="p">,</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">qseqlen</span><span class="p">,</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"> <span class="n" style="color: #333;">query_head</span><span class="p">,</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">query_head_len</span><span class="p">,</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"> <span class="n" style="color: #333;">query_qual_fwd</span><span class="p">,</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">qsize</span><span class="p">,</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">);</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="p">}</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">count_rev</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_count</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">count_rev</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_factor</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">count_fwd</span><span class="p">))</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"> <span class="p">{</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* rev */</span></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="n" style="color: #333;">matches_rev</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* alloc more mem if necessary to keep reverse sequence and qual */</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)(</span><span class="n" style="color: #333;">qseqlen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alloc</span><span class="p">)</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="p">{</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">alloc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseqlen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="n" style="color: #333;">qseq_rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">xrealloc</span><span class="p">(</span><span class="n" style="color: #333;">qseq_rev</span><span class="p">,</span> <span class="n" style="color: #333;">alloc</span><span class="p">);</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastx_is_fastq</span><span class="p">(</span><span class="n" style="color: #333;">query_h</span><span class="p">))</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="n" style="color: #333;">query_qual_rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">xrealloc</span><span class="p">(</span><span class="n" style="color: #333;">query_qual_rev</span><span class="p">,</span> <span class="n" style="color: #333;">alloc</span><span class="p">);</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="p">}</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* get reverse complementary sequence */</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">reverse_complement</span><span class="p">(</span><span class="n" style="color: #333;">qseq_rev</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_fwd</span><span class="p">,</span> <span class="n" style="color: #333;">qseqlen</span><span class="p">);</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastaout</span><span class="p">)</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">fasta_print_general</span><span class="p">(</span><span class="n" style="color: #333;">fp_fastaout</span><span class="p">,</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">qseq_rev</span><span class="p">,</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">qseqlen</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="n" style="color: #333;">query_head</span><span class="p">,</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">query_head_len</span><span class="p">,</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">qsize</span><span class="p">,</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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296
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastqout</span><span class="p">)</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="p">{</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* reverse quality scores */</span></span>
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300
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastx_is_fastq</span><span class="p">(</span><span class="n" style="color: #333;">query_h</span><span class="p">))</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="p">{</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">qseqlen</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">query_qual_rev</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query_qual_fwd</span><span class="p">[</span><span class="n" style="color: #333;">qseqlen</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <span class="n" style="color: #333;">query_qual_rev</span><span class="p">[</span><span class="n" style="color: #333;">qseqlen</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="p">}</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"> <span class="n" style="color: #333;">fastq_print_general</span><span class="p">(</span><span class="n" style="color: #333;">fp_fastqout</span><span class="p">,</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"> <span class="n" style="color: #333;">qseq_rev</span><span class="p">,</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"> <span class="n" style="color: #333;">qseqlen</span><span class="p">,</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="n" style="color: #333;">query_head</span><span class="p">,</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">query_head_len</span><span class="p">,</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"> <span class="n" style="color: #333;">query_qual_rev</span><span class="p">,</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">qsize</span><span class="p">,</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">);</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="p">}</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="p">}</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> <span class="p">{</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* undecided */</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">notmatched</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_notmatched</span><span class="p">)</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="p">{</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastx_is_fastq</span><span class="p">(</span><span class="n" style="color: #333;">query_h</span><span class="p">))</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">fastq_print_general</span><span class="p">(</span><span class="n" style="color: #333;">fp_notmatched</span><span class="p">,</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">qseq_fwd</span><span class="p">,</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"> <span class="n" style="color: #333;">qseqlen</span><span class="p">,</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="n" style="color: #333;">query_head</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"> <span class="n" style="color: #333;">query_head_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="n" style="color: #333;">query_qual_fwd</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;">qsize</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"> <span class="n" style="color: #333;">notmatched</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">fasta_print_general</span><span class="p">(</span><span class="n" style="color: #333;">fp_notmatched</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">qseq_fwd</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="n" style="color: #333;">qseqlen</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">query_head</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">query_head_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">qsize</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">notmatched</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_tabbedout</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_tabbedout</span><span class="p">,</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%c</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">query_head</span><span class="p">,</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">'+'</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">'-'</span> <span class="o" style="font-weight: 600;">:</span> <span class="sc" style="color: #d14;">'?'</span><span class="p">),</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">count_fwd</span><span class="p">,</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="n" style="color: #333;">count_rev</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* show progress */</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_update</span><span class="p">(</span><span class="n" style="color: #333;">progress</span><span class="p">);</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_done</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* clean up */</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qseq_rev</span><span class="p">)</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">qseq_rev</span><span class="p">);</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">query_qual_rev</span><span class="p">)</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">query_qual_rev</span><span class="p">);</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="n" style="color: #333;">unique_exit</span><span class="p">(</span><span class="n" style="color: #333;">uh_fwd</span><span class="p">);</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="n" style="color: #333;">dbindex_free</span><span class="p">();</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="n" style="color: #333;">db_free</span><span class="p">();</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_tabbedout</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp_tabbedout</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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_notmatched</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp_notmatched</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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastqout</span><span class="p">)</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp_fastqout</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastaout</span><span class="p">)</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fp_fastaout</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>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="n" style="color: #333;">fasta_close</span><span class="p">(</span><span class="n" style="color: #333;">query_h</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>
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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;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt_quiet</span><span class="p">)</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="p">{</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Forward oriented sequences: %d"</span><span class="p">,</span> <span class="n" style="color: #333;">matches_fwd</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matches_fwd</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Reverse oriented sequences: %d"</span><span class="p">,</span> <span class="n" style="color: #333;">matches_rev</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matches_rev</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"All oriented sequences: %d"</span><span class="p">,</span> <span class="n" style="color: #333;">qmatches</span><span class="p">);</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Not oriented sequences: %d"</span><span class="p">,</span> <span class="n" style="color: #333;">notmatched</span><span class="p">);</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">notmatched</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Total number of sequences: %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="p">}</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_log</span><span class="p">)</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"> <span class="p">{</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Forward oriented sequences: %d"</span><span class="p">,</span> <span class="n" style="color: #333;">matches_fwd</span><span class="p">);</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matches_fwd</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Reverse oriented sequences: %d"</span><span class="p">,</span> <span class="n" style="color: #333;">matches_rev</span><span class="p">);</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matches_rev</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"All oriented sequences: %d"</span><span class="p">,</span> <span class="n" style="color: #333;">qmatches</span><span class="p">);</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Not oriented sequences: %d"</span><span class="p">,</span> <span class="n" style="color: #333;">notmatched</span><span class="p">);</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">notmatched</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Total number of sequences: %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="p">}</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#f5a353284fc2c13a1d86de119b77e52c00961dad"><strong>src/orient.h</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> VSEARCH: a versatile open source tool for metagenomics</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2014-2021, Torbjorn Rognes, Frederic Mahe and Tomas Flouri</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> All rights reserved.</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Contact: Torbjorn Rognes <torognes@ifi.uio.no>,</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Department of Informatics, University of Oslo,</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> PO Box 1080 Blindern, NO-0316 Oslo, Norway</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This software is dual-licensed and available under a choice</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> of one of two licenses, either under the terms of the GNU</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> General Public License version 3 or the BSD 2-Clause License.</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> GNU General Public License version 3</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This program is free software: you can redistribute it and/or modify</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> it under the terms of the GNU General Public License as published by</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> the Free Software Foundation, either version 3 of the License, or</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> (at your option) any later version.</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This program is distributed in the hope that it will be useful,</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> GNU General Public License for more details.</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> You should have received a copy of the GNU General Public License</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> The BSD 2-Clause License</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Redistribution and use in source and binary forms, with or without</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> modification, are permitted provided that the following conditions</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> are met:</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> 1. Redistributions of source code must retain the above copyright</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> notice, this list of conditions and the following disclaimer.</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> 2. Redistributions in binary form must reproduce the above copyright</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> notice, this list of conditions and the following disclaimer in the</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> documentation and/or other materials provided with the distribution.</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> POSSIBILITY OF SUCH DAMAGE.</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">orient</span><span class="p">();</span></span></pre>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#86db155668a2aba91ba2f6297398674549d9252a"><strong>src/otutable.cc</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">@@ -392,7 +392,7 @@ void otutable_print_biomout(FILE * fp)</td>
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"null"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"{</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span>"</span><span class="s" style="color: #d14;">taxonomy</span><span class="se" style="color: #d14;"><span class="idiff">\</span>"</span><span class="s" style="color: #d14;">:</span><span class="se" style="color: #d14;"><span class="idiff right">\</span>"</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">R"({</span>"taxonomy":"<span class="idiff right">)</span>"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp"> <span class="n" style="color: #333;">otu_tax_map_t</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">otutable</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">otu_tax_map</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">otu_name</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">otutable</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">otu_tax_map</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#7c0ab125929a2525691761258411d8c080de4e02"><strong>src/search.cc</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">@@ -689,24 +689,40 @@ void usearch_global(char * cmdline, char * progheader)</td>
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt_quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching unique query sequences: %d of %d (%.2f%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching unique query sequences: %d of %d"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_sizein</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching total query sequences: %"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" of %"</span></span>
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="cpp"> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" (%.2f%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches_abundance</span><span class="p">,</span> <span class="n" style="color: #333;">queries_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches_abundance</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries_abundance</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching total query sequences: %"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" of %"</span></span>
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="cpp"> <span class="n" style="color: #333;">PRIu64</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches_abundance</span><span class="p">,</span> <span class="n" style="color: #333;">queries_abundance</span><span class="p">);</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries_abundance</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches_abundance</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries_abundance</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_log</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching unique query sequences: %d of %d (%.2f%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching unique query sequences: %d of %d"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_sizein</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching total query sequences: %"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" of %"</span></span>
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="cpp"> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" (%.2f%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches_abundance</span><span class="p">,</span> <span class="n" style="color: #333;">queries_abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches_abundance</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries_abundance</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp"> <span class="p">{</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching total query sequences: %"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" of %"</span></span>
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="cpp"> <span class="n" style="color: #333;">PRIu64</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches_abundance</span><span class="p">,</span> <span class="n" style="color: #333;">queries_abundance</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries_abundance</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="cpp"> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches_abundance</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries_abundance</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_biomout</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#38a97b74048ec78f8a80be22b7af7ae63ac895a1"><strong>src/searchexact.cc</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">@@ -709,12 +709,20 @@ void search_exact(char * cmdline, char * progheader)</td>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="cpp"> <span class="n" style="color: #333;">fasta_close</span><span class="p">(</span><span class="n" style="color: #333;">query_fasta_h</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt_quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching query sequences: %d of %d (%.2f%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching query sequences: %d of %d"</span><span class="p">,</span> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_log</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching query sequences: %d of %d (%.2f%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="cpp"> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Matching query sequences: %d of %d"</span><span class="p">,</span> <span class="n" style="color: #333;">qmatches</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qmatches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fp_biomout</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="cpp"> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#20b2f8db5b4d6b8a208f67d263ba9782b8d7657e"><strong>src/sintax.cc</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">@@ -319,17 +319,9 @@ void sintax_analyse(char * query_head,</td>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">sintax_query</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">t</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">all_seqno</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="n" style="color: #333;">bootstrap_count</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">best_seqno</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">boot_count</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">best_count</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">best_count</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">best_count</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="cpp"> <span class="n" style="color: #333;">best_seqno</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">best_seqno</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">boot_count</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="cpp"> <span class="n" style="color: #333;">boot_count</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">best_seqno</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">};</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">boot_count</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">best_count</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">};</span></span>
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qseqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">si_plus</span><span class="p">[</span><span class="n" style="color: #333;">t</span><span class="p">].</span><span class="n" style="color: #333;">qseqlen</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">query_head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">si_plus</span><span class="p">[</span><span class="n" style="color: #333;">t</span><span class="p">].</span><span class="n" style="color: #333;">query_head</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -628,12 +620,20 @@ void sintax()</td>
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_done</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">opt_quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Classified %d of %d sequences (%.2f%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="cpp"> <span class="n" style="color: #333;">classified</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">classified</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Classified %d of %d sequences"</span><span class="p">,</span> <span class="n" style="color: #333;">classified</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">classified</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_log</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Classified %d of %d sequences (%.2f%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="cpp"> <span class="n" style="color: #333;">classified</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">classified</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"Classified %d of %d sequences"</span><span class="p">,</span> <span class="n" style="color: #333;">classified</span><span class="p">,</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">" (%.2f%%)"</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">classified</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">queries</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* clean up */</span></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#b0109d980457466d1deec0f79c45e2b54114fdd5"><strong>src/vsearch.cc</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">@@ -150,6 +150,7 @@ char * opt_msaout;</td>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_nonchimeras</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_notmatched</span><span class="p">;</span></span>
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152
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_notmatchedfq</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_orient</span><span class="p">;</span></span>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_otutabout</span><span class="p">;</span></span>
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_output</span><span class="p">;</span></span>
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_pattern</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -817,6 +818,7 @@ void args_init(int argc, char **argv)</td>
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817
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818
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_notmatched</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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818
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819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_notmatched</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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819
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820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_notrunclabels</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_orient</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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822
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_otutabout</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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821
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823
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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822
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824
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_output_no_hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -879,7 +881,7 @@ void args_init(int argc, char **argv)</td>
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879
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881
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<pre style="margin: 0;"> <span id="LC881" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_usersort</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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880
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882
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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881
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883
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_weak_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">10.0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC882" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_wordlength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">8</span></span><span class="p">;</span></span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_wordlength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span></span>
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883
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885
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_xn</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">8.0</span><span class="p">;</span></span>
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886
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_xsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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887
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_xee</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1044,6 +1046,7 @@ void args_init(int argc, char **argv)</td>
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1044
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1046
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<pre style="margin: 0;"> <span id="LC1046" class="line" lang="cpp"> <span class="n" style="color: #333;">option_notmatched</span><span class="p">,</span></span>
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1045
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1047
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<pre style="margin: 0;"> <span id="LC1047" class="line" lang="cpp"> <span class="n" style="color: #333;">option_notmatchedfq</span><span class="p">,</span></span>
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1046
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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;">option_notrunclabels</span><span class="p">,</span></span>
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1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="cpp"> <span class="n" style="color: #333;">option_orient</span><span class="p">,</span></span>
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1047
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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;">option_otutabout</span><span class="p">,</span></span>
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1048
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1051
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="cpp"> <span class="n" style="color: #333;">option_output</span><span class="p">,</span></span>
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1049
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1052
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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="cpp"> <span class="n" style="color: #333;">option_output_no_hits</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1273,6 +1276,7 @@ void args_init(int argc, char **argv)</td>
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1273
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<pre style="margin: 0;"> <span id="LC1276" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"notmatched"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1274
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1277
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<pre style="margin: 0;"> <span id="LC1277" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"notmatchedfq"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1275
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1278
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<pre style="margin: 0;"> <span id="LC1278" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"notrunclabels"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"orient"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1276
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1280
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<pre style="margin: 0;"> <span id="LC1280" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"otutabout"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1277
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1281
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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"output"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1278
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<td class="new_line diff-line-num" data-linenumber="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1282
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<pre style="margin: 0;"> <span id="LC1282" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"output_no_hits"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2295,6 +2299,10 @@ void args_init(int argc, char **argv)</td>
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2295
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2299
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<pre style="margin: 0;"> <span id="LC2299" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_derep_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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2296
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<td class="new_line diff-line-num" data-linenumber="2300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2300
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<pre style="margin: 0;"> <span id="LC2300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2297
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2301
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<pre style="margin: 0;"> <span id="LC2301" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="2298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2302
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<pre style="margin: 0;">+<span id="LC2302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">option_orient</span><span class="p">:</span></span>
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2303
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<pre style="margin: 0;">+<span id="LC2303" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_orient</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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2304
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<pre style="margin: 0;">+<span id="LC2304" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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2305
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<pre style="margin: 0;">+<span id="LC2305" class="line" lang="cpp"></span>
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2298
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2306
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<pre style="margin: 0;"> <span id="LC2306" class="line" lang="cpp"> <span class="nl">default:</span></span>
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2299
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2307
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<pre style="margin: 0;"> <span id="LC2307" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Internal error in option parsing"</span><span class="p">);</span></span>
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2300
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2308
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<pre style="margin: 0;"> <span id="LC2308" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2340,6 +2348,7 @@ void args_init(int argc, char **argv)</td>
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2340
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2348
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<pre style="margin: 0;"> <span id="LC2348" class="line" lang="cpp"> <span class="n" style="color: #333;">option_help</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="2341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2341
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<td class="new_line diff-line-num" data-linenumber="2349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2349
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<pre style="margin: 0;"> <span id="LC2349" class="line" lang="cpp"> <span class="n" style="color: #333;">option_makeudb_usearch</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="2342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2342
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2350
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<pre style="margin: 0;"> <span id="LC2350" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maskfasta</span><span class="p">,</span></span>
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2351
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<pre style="margin: 0;">+<span id="LC2351" class="line" lang="cpp"> <span class="n" style="color: #333;">option_orient</span><span class="p">,</span></span>
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2343
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2352
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<pre style="margin: 0;"> <span id="LC2352" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rereplicate</span><span class="p">,</span></span>
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2344
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2353
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<pre style="margin: 0;"> <span id="LC2353" class="line" lang="cpp"> <span class="n" style="color: #333;">option_search_exact</span><span class="p">,</span></span>
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2345
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2354
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<pre style="margin: 0;"> <span id="LC2354" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sff_convert</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3398,6 +3407,34 @@ void args_init(int argc, char **argv)</td>
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3398
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<td class="new_line diff-line-num" data-linenumber="3407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3407
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<pre style="margin: 0;"> <span id="LC3407" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="3399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3399
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3408
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<pre style="margin: 0;"> <span id="LC3408" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">},</span></span>
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3400
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3409
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<pre style="margin: 0;"> <span id="LC3409" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="3410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3410
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<pre style="margin: 0;">+<span id="LC3410" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">option_orient</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3411
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<pre style="margin: 0;">+<span id="LC3411" class="line" lang="cpp"> <span class="n" style="color: #333;">option_bzip2_decompress</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3401" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="3412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3412
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<pre style="margin: 0;">+<span id="LC3412" class="line" lang="cpp"> <span class="n" style="color: #333;">option_db</span><span class="p">,</span></span>
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3413
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<pre style="margin: 0;">+<span id="LC3413" class="line" lang="cpp"> <span class="n" style="color: #333;">option_dbmask</span><span class="p">,</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="3414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3414
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<pre style="margin: 0;">+<span id="LC3414" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fasta_width</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3401" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="3415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3415
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<pre style="margin: 0;">+<span id="LC3415" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastaout</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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3416
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<pre style="margin: 0;">+<span id="LC3416" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastqout</span><span class="p">,</span></span>
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3417
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<pre style="margin: 0;">+<span id="LC3417" class="line" lang="cpp"> <span class="n" style="color: #333;">option_gzip_decompress</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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3418
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<pre style="margin: 0;">+<span id="LC3418" class="line" lang="cpp"> <span class="n" style="color: #333;">option_log</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3419
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<pre style="margin: 0;">+<span id="LC3419" class="line" lang="cpp"> <span class="n" style="color: #333;">option_no_progress</span><span class="p">,</span></span>
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3420
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<pre style="margin: 0;">+<span id="LC3420" class="line" lang="cpp"> <span class="n" style="color: #333;">option_notmatched</span><span class="p">,</span></span>
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3421
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<pre style="margin: 0;">+<span id="LC3421" class="line" lang="cpp"> <span class="n" style="color: #333;">option_notrunclabels</span><span class="p">,</span></span>
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3422
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<pre style="margin: 0;">+<span id="LC3422" class="line" lang="cpp"> <span class="n" style="color: #333;">option_qmask</span><span class="p">,</span></span>
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3423
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<pre style="margin: 0;">+<span id="LC3423" class="line" lang="cpp"> <span class="n" style="color: #333;">option_quiet</span><span class="p">,</span></span>
</pre>
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3424
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<pre style="margin: 0;">+<span id="LC3424" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
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3425
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<pre style="margin: 0;">+<span id="LC3425" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3426
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<pre style="margin: 0;">+<span id="LC3426" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="3427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3427
</td>
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<pre style="margin: 0;">+<span id="LC3427" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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3428
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<pre style="margin: 0;">+<span id="LC3428" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
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3429
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<pre style="margin: 0;">+<span id="LC3429" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
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3430
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<pre style="margin: 0;">+<span id="LC3430" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
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3431
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<pre style="margin: 0;">+<span id="LC3431" class="line" lang="cpp"> <span class="n" style="color: #333;">option_tabbedout</span><span class="p">,</span></span>
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3432
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<pre style="margin: 0;">+<span id="LC3432" class="line" lang="cpp"> <span class="n" style="color: #333;">option_threads</span><span class="p">,</span></span>
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3433
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<pre style="margin: 0;">+<span id="LC3433" class="line" lang="cpp"> <span class="n" style="color: #333;">option_wordlength</span><span class="p">,</span></span>
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3434
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<pre style="margin: 0;">+<span id="LC3434" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xee</span><span class="p">,</span></span>
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3435
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<pre style="margin: 0;">+<span id="LC3435" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span><span class="p">,</span></span>
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3436
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<pre style="margin: 0;">+<span id="LC3436" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">},</span></span>
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3437
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<pre style="margin: 0;">+<span id="LC3437" class="line" lang="cpp"></span>
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3401
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3438
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<pre style="margin: 0;"> <span id="LC3438" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">option_rereplicate</span><span class="p">,</span></span>
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3402
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3439
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<pre style="margin: 0;"> <span id="LC3439" class="line" lang="cpp"> <span class="n" style="color: #333;">option_bzip2_decompress</span><span class="p">,</span></span>
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3403
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3440
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<pre style="margin: 0;"> <span id="LC3440" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fasta_width</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4004,6 +4041,15 @@ void args_init(int argc, char **argv)</td>
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4004
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4041
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<pre style="margin: 0;"> <span id="LC4041" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_maxrejects</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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4005
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4042
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<pre style="margin: 0;"> <span id="LC4042" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"The argument to --maxrejects must not be negative"</span><span class="p">);</span></span>
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4006
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4043
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<pre style="margin: 0;"> <span id="LC4043" class="line" lang="cpp"></span>
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4044
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<pre style="margin: 0;">+<span id="LC4044" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_wordlength</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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4045
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<pre style="margin: 0;">+<span id="LC4045" class="line" lang="cpp"> <span class="p">{</span></span>
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4046
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<pre style="margin: 0;">+<span id="LC4046" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* set default word length */</span></span>
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4047
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<pre style="margin: 0;">+<span id="LC4047" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_orient</span><span class="p">)</span></span>
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4048
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<pre style="margin: 0;">+<span id="LC4048" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_wordlength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">12</span><span class="p">;</span></span>
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4049
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<pre style="margin: 0;">+<span id="LC4049" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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4050
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<pre style="margin: 0;">+<span id="LC4050" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_wordlength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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4051
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<pre style="margin: 0;">+<span id="LC4051" class="line" lang="cpp"> <span class="p">}</span></span>
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4052
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<pre style="margin: 0;">+<span id="LC4052" class="line" lang="cpp"></span>
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4007
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4053
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<pre style="margin: 0;"> <span id="LC4053" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">opt_wordlength</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">opt_wordlength</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">15</span><span class="p">))</span></span>
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4008
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4054
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<pre style="margin: 0;"> <span id="LC4054" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"The argument to --wordlength must be in the range 3 to 15"</span><span class="p">);</span></span>
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4009
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4055
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<pre style="margin: 0;"> <span id="LC4055" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4410,6 +4456,19 @@ void cmd_help()</td>
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4410
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4456
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<pre style="margin: 0;"> <span id="LC4456" class="line" lang="cpp"> <span class="s" style="color: #d14;">" Output</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4411
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4457
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<pre style="margin: 0;"> <span id="LC4457" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --output FILENAME output to specified FASTA file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4412
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4458
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<pre style="margin: 0;"> <span id="LC4458" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4459
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<pre style="margin: 0;">+<span id="LC4459" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Orient sequences in forward or reverse direction</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4460
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<pre style="margin: 0;">+<span id="LC4460" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --orient FILENAME orient sequences in given FASTA/FASTQ file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4461
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<pre style="margin: 0;">+<span id="LC4461" class="line" lang="cpp"> <span class="s" style="color: #d14;">" Data</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4462
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<pre style="margin: 0;">+<span id="LC4462" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --db FILENAME database of sequences in correct orientation</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4463
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<pre style="margin: 0;">+<span id="LC4463" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --dbmask none|dust|soft mask db seqs with dust, soft or no method (dust)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4464
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<pre style="margin: 0;">+<span id="LC4464" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --qmask none|dust|soft mask query with dust, soft or no method (dust)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4465
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<pre style="margin: 0;">+<span id="LC4465" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --wordlength INT length of words used for matching 3-15 (12)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4466
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<pre style="margin: 0;">+<span id="LC4466" class="line" lang="cpp"> <span class="s" style="color: #d14;">" Output</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4467
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<pre style="margin: 0;">+<span id="LC4467" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastaout FILENAME FASTA output filename for oriented sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4468
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<pre style="margin: 0;">+<span id="LC4468" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastqout FILENAME FASTQ output filenamr for oriented sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4469
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<pre style="margin: 0;">+<span id="LC4469" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --notmatched FILENAME output filename for undetermined sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4470
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<pre style="margin: 0;">+<span id="LC4470" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --tabbedout FILENAME output filename for result information</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4471
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<pre style="margin: 0;">+<span id="LC4471" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4413
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4472
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<pre style="margin: 0;"> <span id="LC4472" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Paired-end reads joining</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4414
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4473
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<pre style="margin: 0;"> <span id="LC4473" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastq_join FILENAME join paired-end reads into one sequence with gap</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4415
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4474
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<pre style="margin: 0;"> <span id="LC4474" class="line" lang="cpp"> <span class="s" style="color: #d14;">" Data</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5097,6 +5156,8 @@ int main(int argc, char** argv)</td>
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5097
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5156
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<pre style="margin: 0;"> <span id="LC5156" class="line" lang="cpp"> <span class="n" style="color: #333;">fastx_getsubseq</span><span class="p">();</span></span>
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5098
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5157
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<pre style="margin: 0;"> <span id="LC5157" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_cut</span><span class="p">)</span></span>
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5099
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5158
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<pre style="margin: 0;"> <span id="LC5158" class="line" lang="cpp"> <span class="n" style="color: #333;">cut</span><span class="p">();</span></span>
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5159
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<pre style="margin: 0;">+<span id="LC5159" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_orient</span><span class="p">)</span></span>
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5160
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<pre style="margin: 0;">+<span id="LC5160" class="line" lang="cpp"> <span class="n" style="color: #333;">orient</span><span class="p">();</span></span>
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5100
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5161
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<pre style="margin: 0;"> <span id="LC5161" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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5101
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5162
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<pre style="margin: 0;"> <span id="LC5162" class="line" lang="cpp"> <span class="n" style="color: #333;">cmd_none</span><span class="p">();</span></span>
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5102
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5163
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<pre style="margin: 0;"> <span id="LC5163" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/87aafc8e9fce863b18df0eb6ace9584d0d947be4...ec00cc2b87f375288fb74e899705cf65eff113c0#d5c50f833cab4828d6d2b3f54dda35a42237db09"><strong>src/vsearch.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -255,6 +255,7 @@</td>
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255
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "sffconvert.h"</span></span>
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "getseq.h"</span></span>
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257
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "cut.h"</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "orient.h"</span></span>
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258
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="c"></span>
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259
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* options */</span></span>
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -346,6 +347,7 @@ extern char * opt_msaout;</td>
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346
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_nonchimeras</span><span class="p">;</span></span>
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347
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_notmatched</span><span class="p">;</span></span>
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348
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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_notmatchedfq</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_orient</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_otutabout</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_output</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt_pattern</span><span class="p">;</span></span>
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