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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/43f7534f734bb64bcbb3512adad0fd7ac21acf5d">43f7534f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-09-20T19:47:16+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.15.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vsearch/-/commit/97c0d457061aee3717826d972f29d1c3068c1314">97c0d457</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-09-20T19:47:17+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.15.0'
Update to upstream version '2.15.0'
with Debian dir 3ccf7154ef6af28f7c58dcfd03ae8be50c701f59</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vsearch/-/commit/9815f033f117767b6ced6662fbc1b3914cd13a91">9815f033</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-09-20T20:34:50+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove reference data, compare checksum
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vsearch/-/commit/1a58654f7d79616fe84aa91161719aa8a6f51f44">1a58654f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-09-20T20:36:56+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vsearch/-/commit/91780227165a2cd116ba9198a8bf8990fca730d9">91780227</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-09-20T20:37:25+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
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<h4>23 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#8fff93012d334f4517b4ff248a8becd742f29357">
<span class="deleted-file">
−
debian/tests/expected-output/test1-expected.out
</span>
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<li class="file-stats">
<a href="#39124f06084a2764a0d57245dba1893d205e7340">
<span class="deleted-file">
−
debian/tests/expected-output/test2-expected.out
</span>
</a>
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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</li>
<li class="file-stats">
<a href="#d2c3ee3c7e4475729b657183f658c0c046c5413b">
debian/vsearch-examples.docs
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<li class="file-stats">
<a href="#e9eacc068eb0149cb6567e67eb35ca6a728c05af">
man/Makefile.am
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<li class="file-stats">
<a href="#b7ca4efea9812be2ea989e558de10e419bd9cf39">
man/vsearch.1
</a>
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<li class="file-stats">
<a href="#d79e6705e3db119ee1bb6ad9670fe99b162c13b0">
src/cluster.cc
</a>
</li>
<li class="file-stats">
<a href="#e0f36bd5084cd7076742276f78c5e2d9d62127df">
src/derep.cc
</a>
</li>
<li class="file-stats">
<a href="#8f8dff040d7feb7206c5df2f516c3df968e7268b">
src/derep.h
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<li class="file-stats">
<a href="#67ef99e491c4bda5d0c47f152cae53d18d7fbcd3">
src/fasta.cc
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<li class="file-stats">
<a href="#d6ab431461af8e07f1ea378788017353266e8ba2">
src/fastq.cc
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<li class="file-stats">
<a href="#6f963d02896322eab19500836bca3f9a22619a35">
src/fastqops.cc
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<li class="file-stats">
<a href="#66934cf2fb3d65e60500632c125c6324b6bebbec">
src/fastx.cc
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<li class="file-stats">
<a href="#5d506abf37fc32f1877a3abd29631760d6209ba5">
src/maps.cc
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<li class="file-stats">
<a href="#9c689a31237f70b17e9bac31f42d1b22ea1d59be">
src/mergepairs.cc
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<li class="file-stats">
<a href="#20b2f8db5b4d6b8a208f67d263ba9782b8d7657e">
src/sintax.cc
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</li>
<li class="file-stats">
<a href="#a9f0536a1f6138188dbd33cace26c5ff3c05cb39">
src/sortbylength.cc
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<li class="file-stats">
<a href="#28d5028d98d0db6236ac6ceb7aa6d9237356403c">
src/sortbysize.cc
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<li class="file-stats">
<a href="#b0109d980457466d1deec0f79c45e2b54114fdd5">
src/vsearch.cc
</a>
</li>
<li class="file-stats">
<a href="#d5c50f833cab4828d6d2b3f54dda35a42237db09">
src/vsearch.h
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</li>
</ul>
<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,7 +34,7 @@ Most of the nucleotide based commands and options in USEARCH version 7 are suppo</td>
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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Getting Help</span></span>
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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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">4.2</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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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="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">5.0</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>
</pre>
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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Example</span></span>
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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"></span>
</pre>
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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,9 +47,9 @@ 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="LC47" 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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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC49" 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">4.2</span>.tar.gz</span>
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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown">tar xzf v2.1<span class="idiff left right">4.2</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">4.2</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">5.0</span>.tar.gz</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown">tar xzf v2.1<span class="idiff left right">5.0</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">5.0</span></span>
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53
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown">./autogen.sh</span>
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown">./configure</span>
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55
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown">make</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -78,43 +78,43 @@ Binary distributions are provided for x86-64 systems running GNU/Linux, macOS (v</td>
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78
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<pre style="margin: 0;"> <span id="LC78" 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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79
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown"></span>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
</pre>
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81
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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 right">4.2/vsearch-2.14.2</span>-linux-x86_64.tar.gz</span>
</pre>
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82
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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">4.2</span>-linux-x86_64.tar.gz</span>
</pre>
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81
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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 right">5.0/vsearch-2.15.0</span>-linux-x86_64.tar.gz</span>
</pre>
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82
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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">5.0</span>-linux-x86_64.tar.gz</span>
</pre>
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83
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"><span class="p">```</span></span>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"></span>
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85
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85
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<pre style="margin: 0;"> <span id="LC85" 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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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"></span>
</pre>
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87
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87
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<pre style="margin: 0;"> <span id="LC87" 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 right">4.2/vsearch-2.14.2</span>-linux-ppc64le.tar.gz</span>
</pre>
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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">4.2</span>-linux-ppc64le.tar.gz</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 right">5.0/vsearch-2.15.0</span>-linux-ppc64le.tar.gz</span>
</pre>
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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">5.0</span>-linux-ppc64le.tar.gz</span>
</pre>
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90
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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91
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"></span>
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92
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92
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<pre style="margin: 0;"> <span id="LC92" 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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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"></span>
</pre>
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94
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
</pre>
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95
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<td class="diff-line-num new_line old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left right">4.2/vsearch-2.14.2</span>-linux-aarch64.tar.gz</span>
</pre>
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96
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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">4.2</span>-linux-aarch64.tar.gz</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<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 right">5.0/vsearch-2.15.0</span>-linux-aarch64.tar.gz</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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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">5.0</span>-linux-aarch64.tar.gz</span>
</pre>
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97
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<td class="diff-line-num new_line" 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>
</pre>
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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown">Or these commands if you are using a Mac:</span>
</pre>
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100
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
102
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<td class="diff-line-num new_line old" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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 right">4.2/vsearch-2.14.2</span>-macos-x86_64.tar.gz</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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">4.2</span>-macos-x86_64.tar.gz</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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 right">5.0/vsearch-2.15.0</span>-macos-x86_64.tar.gz</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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">5.0</span>-macos-x86_64.tar.gz</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
104
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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
105
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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
105
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC105" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
106
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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="markdown">Or if you are using Windows, download and extract (unzip) the contents of this file:</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
107
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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
107
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
108
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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
108
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
109
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<td class="diff-line-num new_line old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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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 right">4.2/vsearch-2.14.2</span>-win-x86_64.zip</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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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 right">5.0/vsearch-2.15.0</span>-win-x86_64.zip</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
110
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<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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111
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<td class="diff-line-num new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
111
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"></span>
</pre>
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112
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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">4.2-linux-x86_64`</span></span><span class="idiff"> or </span><span class="sb" style="color: #d14;"><span class="idiff right">`vsearch-2.14.2</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="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">5.0-linux-x86_64`</span></span><span class="idiff"> or </span><span class="sb" style="color: #d14;"><span class="idiff right">`vsearch-2.15.0</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="LC113" 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">4.2</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="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">5.0</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="LC115" class="line" lang="markdown"></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="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">4.2/vsearch_manual.pdf</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">) will be generated by </span><span class="sb" style="color: #d14;"><span class="idiff">`make`</span></span><span class="idiff">. To install the manpage manually, copy the </span><span class="sb" style="color: #d14;"><span class="idiff">`vsearch.1`</span></span><span class="idiff"> file or a create a symbolic link to </span><span class="sb" style="color: #d14;"><span class="idiff">`vsearch.1`</span></span><span class="idiff"> in a folder included in your </span><span class="sb" style="color: #d14;"><span class="idiff">`$MANPATH`</span></span><span class="idiff">. The manual in both formats is also available with the binary distribution. The manual in PDF form (</span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">vsearch_manual.pdf</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">https://github.com/torognes/vsearch/releases/download/v2.14.2</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="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">5.0/vsearch_manual.pdf</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">) will be generated by </span><span class="sb" style="color: #d14;"><span class="idiff">`make`</span></span><span class="idiff">. To install the manpage manually, copy the </span><span class="sb" style="color: #d14;"><span class="idiff">`vsearch.1`</span></span><span class="idiff"> file or a create a symbolic link to </span><span class="sb" style="color: #d14;"><span class="idiff">`vsearch.1`</span></span><span class="idiff"> in a folder included in your </span><span class="sb" style="color: #d14;"><span class="idiff">`$MANPATH`</span></span><span class="idiff">. The manual in both formats is also available with the binary distribution. The manual in PDF form (</span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">vsearch_manual.pdf</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">https://github.com/torognes/vsearch/releases/download/v2.15.0</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="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="LC120" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Packages, plugins, and wrappers</span></span>
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<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#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">4.2</span>], [torognes@ifi.uio.no])</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">5.0</span>], [torognes@ifi.uio.no])</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/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">vsearch (2.15.0-1) unstable; urgency=medium</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"> * New upstream version 2.15.0</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Remove reference data, compare checksum</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 <npatra974@gmail.com> Sun, 20 Sep 2020 20:37:25 +0530</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">vsearch (2.14.2-3) unstable; urgency=medium</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"> * Source-only upload</span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#8fff93012d334f4517b4ff248a8becd742f29357"><strong>debian/tests/expected-output/test1-expected.out</strong>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#39124f06084a2764a0d57245dba1893d205e7340"><strong>debian/tests/expected-output/test2-expected.out</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">vsearch --usearch_global query.fsa --db BioMarKs50k.fsa --id 0.9 --alnout test2.out</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">vsearch v2.14.2_linux_x86_64, 7.5GB RAM, 8 cores</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">Query >60caa38f93eb4a7ef8c0fa4d96a5a5f8;size=24</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> %Id TLen Target</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">100% 380 60caa38f93eb4a7ef8c0fa4d96a5a5f8;size=24</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Query 380nt >60caa38f93eb4a7ef8c0fa4d96a5a5f8;size=24</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Target 380nt >60caa38f93eb4a7ef8c0fa4d96a5a5f8;size=24</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Qry 1 + AGCTCCAATAGCGTATATTAAAATTGTTGCGGTTAAAACGCTCGTAGTTGGATATCTGCTAAGG 64</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Tgt 1 + AGCTCCAATAGCGTATATTAAAATTGTTGCGGTTAAAACGCTCGTAGTTGGATATCTGCTAAGG 64</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Qry 65 + GGTTCCGGTCCTTCCCAGTGAAGAATACGCGGAACTCTTCTTGGCATTTATTCAGGGAAGGTGT 128</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Tgt 65 + GGTTCCGGTCCTTCCCAGTGAAGAATACGCGGAACTCTTCTTGGCATTTATTCAGGGAAGGTGT 128</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Qry 129 + TTGCACTTTGTTGTGTGTCACATGATCTGAATTTTTACTTTGAGGAAATGAGAGTGTTTCAAGC 192</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Tgt 129 + TTGCACTTTGTTGTGTGTCACATGATCTGAATTTTTACTTTGAGGAAATGAGAGTGTTTCAAGC 192</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">Qry 193 + AGGCTTTCGCCGTGAATATGATAGCATGGAATAATAGCACAGGACCCCTTTCCAAAGCTGTTGG 256</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Tgt 193 + AGGCTTTCGCCGTGAATATGATAGCATGGAATAATAGCACAGGACCCCTTTCCAAAGCTGTTGG 256</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">Qry 257 + TTTTTTGGAACGAGGTAATCAGAATAAGGATAGTTGGGGGTATTCGTATTTAACTGTCAGAGGT 320</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">Tgt 257 + TTTTTTGGAACGAGGTAATCAGAATAAGGATAGTTGGGGGTATTCGTATTTAACTGTCAGAGGT 320</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">Qry 321 + GAAATTCTTGGATTTTTTAAAGACGAACTATTGCGAAGGCATCTGCCCAGGATGTTTTTA 380</span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">Tgt 321 + GAAATTCTTGGATTTTTTAAAGACGAACTATTGCGAAGGCATCTGCCCAGGATGTTTTTA 380</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">380 cols, 380 ids (100.0%), 0 gaps (0.0%)</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -13,14 +13,27 @@ cp /usr/share/doc/${pkg}-examples/* -a "${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>compare_cksum<span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># $1: file whose md5sum needs to be tested</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># $2: expected checksum</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$1</span> | <span class="nb" style="color: #0086b3;">md5sum</span> | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'{print $1}'</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$2</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Checksums do not match"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 1'</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell">vsearch <span class="nt" style="color: #000080;">--cluster_fast</span> BioMarKs50k.fsa <span class="nt" style="color: #000080;">--id</span> 0.97 <span class="nt" style="color: #000080;">--centroids</span> test1.out</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="idiff left">diff </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="idiff right"> test1.out test1-expected.out </span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="idiff left right">compare_cksum test1.out f83633b2f3d9891122056f62b7f4d863</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 2'</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell">vsearch <span class="nt" style="color: #000080;">--usearch_global</span> query.fsa <span class="nt" style="color: #000080;">--db</span> BioMarKs50k.fsa <span class="nt" style="color: #000080;">--id</span> 0.9 <span class="nt" style="color: #000080;">--alnout</span> test2.out</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell">diff <span class="nt" style="color: #000080;">-u</span> <<span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> +3 test2.out<span class="o" style="font-weight: 600;">)</span> <<span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> +3 test2-expected.out<span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> +3 test2.out<span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span> test2_.out</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">compare_cksum test2_.out a84f0fe81dfac71bef52eb715bfb9404</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#d2c3ee3c7e4475729b657183f658c0c046c5413b"><strong>debian/vsearch-examples.docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">debian/tests/data/*</span></pre>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">debian/tests/expected-output/*</span></pre>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#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">@@ -34,7 +34,7 @@ vsearch_manual.pdf : vsearch.1</td>
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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="LC37" 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;">-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="LC37" class="line" lang="make"> groff <span class="nt" style="color: #000080;">-<span class="idiff left">W</span></span><span class="idiff"> space </span><span class="nt" style="color: #000080;"><span class="idiff right">-</span>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="LC38" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC39" 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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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#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 "J<span class="idiff left right">anuary 28, 2020" "version 2.14.2</span>" "USER COMMANDS"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH vsearch 1 "J<span class="idiff left right">une 19, 2020" "version 2.15.0</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,7 +34,7 @@ Clustering:</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">.RE</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">Dereplication and rereplication:</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">.RS</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">\fBvsearch\fR (\-\-derep_fulllength | \-\-derep_prefix)</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fBvsearch\fR (\-\-derep_fulllength | \-\-derep_<span class="idiff left right">id | \-\-derep_</span>prefix)</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">\fIfastafile\fR (\-\-output | \-\-uc) \fIoutputfile\fR [\fIoptions\fR]</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">\fBvsearch\fR \-\-rereplicate \fIfastafile\fR \-\-output</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">@@ -198,17 +198,21 @@ alignment method described by Hirschberg (1975) and Myers and Miller</td>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="plaintext">.SS Input</span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="plaintext">\fBvsearch\fR accept as input fasta or fastq files containing one or</span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="plaintext">several nucleotidic entries. In fasta files, each nucleotidic entry is</span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="plaintext">made of a header and a sequence. The header is defined as the string</span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="plaintext">comprised between the '>' symbol and the first space, tab or the end</span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="plaintext">of the line, whichever comes first. Additionally, if the header</span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="plaintext">matches</span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="plaintext">'>[;]size=\fIinteger\fR;label', '>label;size=\fIinteger\fR;label' or</span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext">'>label;size=\fIinteger\fR[;]', \fBvsearch\fR interpret</span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="plaintext">\fIinteger\fR as the number of occurrences (or abundance) of the</span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="plaintext">sequence in the study. That abundance information is used or created</span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext">during chimera detection, clustering, dereplication, sorting and</span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="plaintext">searching.</span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">several nucleotidic entries. In fasta files, each entry is made of a</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">header and a sequence. The header is defined as the string comprised</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">between the initial '>' symbol and the first space, tab or the end of</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">the line, unless the \-\-notrunclabels option is in effect, in which</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">case the entire line is included. The header should contain printable</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">ascii characters (33-126). The program will terminate with a fatal</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">error if there are unprintable ascii characters. A warning will be</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">issued if non-ascii characters (128-255) are encountered.</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">.PP</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">If the header matches '>[;]size=\fIinteger\fR;label',</span>
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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">'>label;size=\fIinteger\fR;label' or '>label;size=\fIinteger\fR[;]',</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">\fBvsearch\fR interpret \fIinteger\fR as the number of occurrences (or</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">abundance) of the sequence in the study. That abundance information is</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">used or created during chimera detection, clustering, dereplication,</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">sorting and searching.</span>
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212
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="plaintext">.PP</span>
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213
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="plaintext">The sequence is defined as a string of IUPAC symbols</span>
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214
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="plaintext">(ACGTURYSWKMDBHVN), starting after the end of the identifier line and</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="349" style="width: 35px; color: rgba(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">@@ -349,7 +353,8 @@ greater than \fIinteger\fR (50,000 nucleotides by default).</td>
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349
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353
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="plaintext">.BI \-\-minseqlength\~ "positive integer"</span>
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350
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354
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="plaintext">All \fBvsearch\fR operations discard sequences of length smaller than</span>
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351
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="plaintext">\fIinteger\fR: 1 nucleotide by default for sorting or shuffling, 32</span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="plaintext">nucleotides for clustering, dereplication or searching.</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext">nucleotides for clustering and dereplication as well as the commands</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext">\-\-makeudb_usearch, \-\-sintax, and \-\-usearch_global.</span>
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353
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="plaintext">.TAG no_progress</span>
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354
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="plaintext">.TP</span>
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355
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360
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="plaintext">.B \-\-no_progress</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">@@ -358,7 +363,8 @@ Do not show the gradually increasing progress indicator.</td>
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358
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="plaintext">.TP</span>
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359
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="plaintext">.B \-\-notrunclabels</span>
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360
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="plaintext">Do not truncate sequence labels at first space or tab, use the full</span>
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361
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="plaintext">header in output files.</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext">header in output files. Turned off by default for all commands except</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext">the sintax command.</span>
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362
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="plaintext">.TAG quiet</span>
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363
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="plaintext">.TP</span>
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="plaintext">.B \-\-quiet</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">@@ -392,7 +398,7 @@ Input sequences are masked as specified with the \-\-qmask and</td>
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392
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="plaintext">\-\-hardmask options. Masking of the database for reference based</span>
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393
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="plaintext">chimera detection is specified with the \-\-dbmask option.</span>
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394
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="plaintext">.PP</span>
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395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="plaintext">In \fIde novo\fR mode, input fasta file <span class="idiff left right">should</span> present abundance</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext">In \fIde novo\fR mode, input fasta file <span class="idiff left right">must</span> present abundance</span>
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396
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="plaintext">annotations (i.e. a pattern [;]size=\fIinteger\fR[;] in the fasta</span>
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397
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="plaintext">header). Input order matters for chimera detection, so we recommend to</span>
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398
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="plaintext">sort sequences by decreasing abundance (default of</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">@@ -437,15 +443,17 @@ parents, or sufficiently close relatives, are not present in the</td>
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437
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443
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="plaintext">database.</span>
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438
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444
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="plaintext">.TAG dn</span>
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439
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445
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="plaintext">.TP</span>
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440
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="plaintext">.BI \-\-dn \0real</span>
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441
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="plaintext">No vote pseudo-count, corresponding to the parameter \fIn\fR in the</span>
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442
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="plaintext">chimera scoring function (default value is 1.4).</span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="plaintext">.BI \-\-dn\~ "strictly positive real number"</span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="plaintext">pseudo-count prior on the number of no votes, corresponding to the</span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="plaintext">parameter \fIn\fR in the chimera scoring function (default value is</span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="plaintext">1.4). Increasing \-\-dn reduces the likelihood of tagging a sequence</span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="plaintext">as a chimera (less false positives, but also more false negatives).</span>
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451
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="plaintext">.TAG fasta_score</span>
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452
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="plaintext">.B \-\-fasta_score</span>
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454
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="plaintext">Add the chimera score to the headers in the fasta output files for</span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="plaintext">chimeras, non-chimeras and borderline sequences, using the<span class="idiff left right"> format</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="plaintext">';uchime_denovo=\fIfloat\fR;'.</span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext">chimeras, non-chimeras and borderline sequences, using the</span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="plaintext"><span class="idiff left right">format </span>';uchime_denovo=\fIfloat\fR;'.</span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="plaintext">.TAG mindiffs</span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="plaintext">.BI \-\-mindiffs\~ "positive integer"</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">@@ -521,8 +529,14 @@ false-positive rate in reference sequences).</td>
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529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="plaintext">When using \-\-uchime_ref, ignore a reference sequence when its</span>
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530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="plaintext">nucleotide sequence is strictly identical to the nucleotidic sequence</span>
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531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="plaintext">of the query.</span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="plaintext">.TAG sizeout</span>
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="plaintext">.B \-\-sizein</span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="plaintext">In \fIde novo\fR mode, abundance annotations</span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="plaintext">(pattern '[>;]size=\fIinteger\fR[;]') present in sequence headers are</span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="plaintext">taken into account by default (\-\-sizein is always implied). This</span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="plaintext">option is ignored by \-\-uchime_ref.</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="plaintext">.TP</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="plaintext">.TAG sizeout</span>
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526
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="plaintext">.B \-\-sizeout</span>
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="plaintext">When relabelling, add abundance annotations to fasta headers (using</span>
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542
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="plaintext">the format ';size=\fIinteger\fR;').</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">@@ -619,13 +633,15 @@ When using \-\-uchimeout, write chimera detection results using a</td>
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619
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633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="plaintext">17\-field, tab\-separated uchime\-like format (drop the 5th field of</span>
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620
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="plaintext">\-\-uchimeout), compatible with usearch version 5 and earlier</span>
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635
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="plaintext">versions.</span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="plaintext">.TP</span>
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622
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637
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="plaintext">.TAG xn</span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="plaintext">.BI \-\-xn\~ "strictly positive real number"</span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="plaintext">weight of no votes, corresponding to the parameter \fIbeta\fR in the</span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="plaintext">scoring function (default value is 8.0). Increasing \-\-xn reduces the</span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="plaintext">likelihood of tagging a sequence as a chimera (less false positives,</span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="plaintext">but also more false negatives).</span>
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643
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="plaintext">.TP</span>
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624
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="plaintext">.BI \-\-xn \0real</span>
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625
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="plaintext">No vote weight, corresponding to the parameter \fIbeta\fR in the</span>
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626
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="plaintext">scoring function (default value is 8.0).</span>
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627
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644
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="plaintext">.TAG xsize</span>
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628
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="plaintext">.TP</span>
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629
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645
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<pre style="margin: 0;"> <span id="LC645" class="line" lang="plaintext">.B \-\-xsize</span>
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630
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646
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="plaintext">Strip abundance information from the headers when writing the output</span>
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631
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647
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="plaintext">file.</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">@@ -696,12 +712,14 @@ first sequence of the cluster).</td>
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712
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="plaintext">.TP</span>
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697
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713
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="plaintext">.BI \-\-clusterout_id</span>
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698
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714
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="plaintext">Add cluster identifier information to the output files</span>
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699
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="plaintext">when using the \-\-consout and \-\-profile options.</span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="plaintext">when using the \-\-c<span class="idiff left right">entroids, \-\-c</span>onsout and \-\-profile options.</span>
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700
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="plaintext">.TAG clusterout_sort</span>
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701
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717
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="plaintext">.TP</span>
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702
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="plaintext">.BI \-\-clusterout_sort</span>
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703
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="plaintext">Sort output files by decreasing abundance</span>
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704
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="plaintext">when using the \-\-consout, \-\-msaout and \-\-profile options.</span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="plaintext">Sort some output files by decreasing abundance instead of input</span>
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="plaintext">order. It applies to the \-\-consout, \-\-msaout, \-\-profile,</span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="plaintext">\-\-centroids, and \-\-uc options. For \-\-uc, the sorting applies</span>
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="plaintext">only to the centroid information part (the C lines).</span>
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723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="plaintext">.TAG cluster_fast</span>
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706
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724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="plaintext">.TP</span>
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725
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="plaintext">.BI \-\-cluster_fast \0filename</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">@@ -901,8 +919,8 @@ greedy clustering (DGC).</td>
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919
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<pre style="margin: 0;"> <span id="LC919" class="line" lang="plaintext">.TAG sizeout</span>
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902
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920
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<pre style="margin: 0;"> <span id="LC920" class="line" lang="plaintext">.TP</span>
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903
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<pre style="margin: 0;"> <span id="LC921" class="line" lang="plaintext">.B \-\-sizeout</span>
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904
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<pre style="margin: 0;">-<span id="LC904" class="line" lang="plaintext">Add abundance annotations to the output fasta files (add the<span class="idiff left right"> pattern</span></span>
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905
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<pre style="margin: 0;">-<span id="LC905" class="line" lang="plaintext">';size=\fIinteger\fR;' to sequence headers). If \-\-sizein is</span>
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="plaintext">Add abundance annotations to the output fasta files (add the</span>
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="plaintext"><span class="idiff left right">pattern </span>';size=\fIinteger\fR;' to sequence headers). If \-\-sizein is</span>
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906
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924
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<pre style="margin: 0;"> <span id="LC924" class="line" lang="plaintext">specified, abundance annotations are reported to output files, and</span>
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907
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925
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="plaintext">each cluster centroid receives a new abundance value corresponding to</span>
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908
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<td class="diff-line-num new_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
926
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<pre style="margin: 0;"> <span id="LC926" class="line" lang="plaintext">the total abundance of the amplicons included in the cluster</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1010" style="width: 35px; color: rgba(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">@@ -992,6 +1010,12 @@ length and the same string of nucleotides (case insensitive, T and U</td>
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992
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1010
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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="plaintext">are considered the same). See the options \-\-sizein and \-\-sizeout</span>
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<td class="diff-line-num old_line" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
993
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<td class="diff-line-num new_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="plaintext">to take into account and compute abundance values. This command does</span>
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994
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<td class="diff-line-num new_line" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1012
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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="plaintext">not support multithreading.</span>
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<td class="diff-line-num new old_line" data-linenumber="995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="plaintext">.TAG derep_id</span>
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<td class="diff-line-num new new_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="plaintext">.TP 9</span>
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<td class="diff-line-num new new_line" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="plaintext">.BI \-\-derep_id \0filename</span>
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<td class="diff-line-num new new_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="plaintext">Merge strictly identical sequences contained in \fIfilename\fR, as</span>
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<td class="diff-line-num new new_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="plaintext">with the \-\-derep_fulllength command, but the sequence labels</span>
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1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="plaintext">(identifiers) on the header line need to be identical too.</span>
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995
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1019
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<pre style="margin: 0;"> <span id="LC1019" class="line" lang="plaintext">.TAG derep_prefix</span>
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996
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1020
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<pre style="margin: 0;"> <span id="LC1020" class="line" lang="plaintext">.TP</span>
</pre>
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997
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<td class="diff-line-num new_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1021
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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="plaintext">.BI \-\-derep_prefix \0filename</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1021" style="width: 35px; color: rgba(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="1045" style="width: 35px; color: rgba(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">@@ -1021,8 +1045,8 @@ Write the dereplicated sequences to \fIfilename\fR, in fasta format</td>
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<td class="diff-line-num old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1021
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<td class="diff-line-num new_line" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1045
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<pre style="margin: 0;"> <span id="LC1045" class="line" lang="plaintext">and sorted by decreasing abundance. Identical sequences receive the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1022
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<td class="diff-line-num 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">
1046
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1046" class="line" lang="plaintext">header of the first sequence of their group. If \-\-sizeout is used,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1023
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<td class="diff-line-num new_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1047
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1047" class="line" lang="plaintext">the number of occurrences (i.e. abundance) of each sequence is</span>
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<td class="diff-line-num old old_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1024
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<td class="diff-line-num new_line old" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1024" class="line" lang="plaintext">indicated at the end of their fasta header using the<span class="idiff left right"> pattern</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1025
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<td class="diff-line-num new_line old" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1025" class="line" lang="plaintext">';size=\fIinteger\fR;'.</span>
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<td class="diff-line-num new old_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="plaintext">indicated at the end of their fasta header using the</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="plaintext"><span class="idiff left right">pattern </span>';size=\fIinteger\fR;'.</span>
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<td class="diff-line-num old_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1026
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<td class="diff-line-num new_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1050
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<pre style="margin: 0;"> <span id="LC1050" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1027
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<td class="diff-line-num new_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1051
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="plaintext">.TAG relabel</span>
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1028
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1052
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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="plaintext">.BI \-\-relabel \0string</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1091" style="width: 35px; color: rgba(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">@@ -1067,8 +1091,8 @@ headers). That option is active by default when rereplicating.</td>
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1067
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1091
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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="plaintext">.TAG sizeout</span>
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1068
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1092
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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="plaintext">.TP</span>
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1069
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1093
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<pre style="margin: 0;"> <span id="LC1093" class="line" lang="plaintext">.B \-\-sizeout</span>
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1070
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<td class="diff-line-num new_line old" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1070" class="line" lang="plaintext">Add abundance annotations to the output fasta file (add the<span class="idiff left right"> pattern</span></span>
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1071
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<pre style="margin: 0;">-<span id="LC1071" class="line" lang="plaintext"><span class="idiff left right">';size=\fIinteger\fR;' to sequence headers). </span> If \-\-sizein is</span>
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1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="plaintext">Add abundance annotations to the output fasta file (add the</span>
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1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="plaintext"><span class="idiff left right">pattern ';size=\fIinteger\fR;' to sequence headers).</span> If \-\-sizein is</span>
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1072
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1096
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<pre style="margin: 0;"> <span id="LC1096" class="line" lang="plaintext">specified, each unique sequence receives a new abundance value</span>
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1073
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1097
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<pre style="margin: 0;"> <span id="LC1097" class="line" lang="plaintext">corresponding to its total abundance (sum of the abundances of its</span>
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1074
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1098
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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="plaintext">occurrences). If \-\-sizein is not specified, input abundances are set</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1537" style="width: 35px; color: rgba(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="1561" style="width: 35px; color: rgba(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">@@ -1537,18 +1561,20 @@ ambiguous bases (N's), as specified with the \-\-fastq_maxns are also</td>
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<td class="diff-line-num old_line" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1537
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1561
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<pre style="margin: 0;"> <span id="LC1561" class="line" lang="plaintext">discarded (no limit by default). Staggered reads are not merged unless</span>
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1538
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1562
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<pre style="margin: 0;"> <span id="LC1562" class="line" lang="plaintext">the \-\-fastq_allowmergestagger option is specified. The minimum</span>
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<td class="diff-line-num old_line" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1539
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<td class="diff-line-num new_line" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1563
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<pre style="margin: 0;"> <span id="LC1563" class="line" lang="plaintext">length of the overlap region between the reads may be specified with</span>
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1540
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<pre style="margin: 0;">-<span id="LC1540" class="line" lang="plaintext">the \-\-fastq_minovlen option (default 10). The overlap region may</span>
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1541
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<pre style="margin: 0;">-<span id="LC1541" class="line" lang="plaintext"><span class="idiff left right">not </span>include more mismatches than specified with the \-\-fastq_maxdiffs</span>
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<td class="diff-line-num new old_line" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1564
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<pre style="margin: 0;">+<span id="LC1564" class="line" lang="plaintext">the \-\-fastq_minovlen option (default 10). The overlap region may<span class="idiff left right"> not</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1565
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<pre style="margin: 0;">+<span id="LC1565" class="line" lang="plaintext">include more mismatches than specified with the \-\-fastq_maxdiffs</span>
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1542
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1566
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<pre style="margin: 0;"> <span id="LC1566" class="line" lang="plaintext">option (10 by default) or a higher percentage of mismatches than</span>
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<td class="diff-line-num old_line" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1543
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1567
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<pre style="margin: 0;"> <span id="LC1567" class="line" lang="plaintext">specified with the \-\-fastq_maxdiffpct option (100.0% by default),</span>
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1544
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1568
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<pre style="margin: 0;"> <span id="LC1568" class="line" lang="plaintext">otherwise the read pair is discarded. Additional rules will avoid</span>
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<td class="diff-line-num old_line" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1545
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1569
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<pre style="margin: 0;"> <span id="LC1569" class="line" lang="plaintext">merging of reads that cannot be aligned reliably and</span>
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<td class="diff-line-num old_line" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1546
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1570
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<pre style="margin: 0;"> <span id="LC1570" class="line" lang="plaintext">unambiguously. The mimimum and maximum length of the merged sequence</span>
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1547
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1571
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<pre style="margin: 0;"> <span id="LC1571" class="line" lang="plaintext">may be specified with the \-\-fastq_minmergelen and</span>
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1548
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<pre style="margin: 0;">-<span id="LC1548" class="line" lang="plaintext">\-\-fastq_maxmergelen options, respectively. Other relevant options</span>
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1549
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<pre style="margin: 0;">-<span id="LC1549" class="line" lang="plaintext">are: \-\-fastq_ascii, \-\-fastq_maxee, \-\-fastq_nostagger,</span>
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1550
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<pre style="margin: 0;">-<span id="LC1550" class="line" lang="plaintext">\-\-fastq_qmax, \-\-fastq_qmaxout, \-\-fastq_qmin, \-\-fastq_qminout,</span>
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1551
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<pre style="margin: 0;">-<span id="LC1551" class="line" lang="plaintext">and \-\-label_suffix.</span>
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1572
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<pre style="margin: 0;">+<span id="LC1572" class="line" lang="plaintext">\-\-fastq_maxmergelen options, respectively. The quality value limits</span>
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1573
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<pre style="margin: 0;">+<span id="LC1573" class="line" lang="plaintext">for output files may be specied with the \-\-fastq_qminout and</span>
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1574
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<pre style="margin: 0;">+<span id="LC1574" class="line" lang="plaintext">\-\-fastq_qmaxout options, but they apply only to the merged region.</span>
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1575
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<pre style="margin: 0;">+<span id="LC1575" class="line" lang="plaintext">Other relevant options are: \-\-fastq_ascii, \-\-fastq_maxee,</span>
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1576
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<pre style="margin: 0;">+<span id="LC1576" class="line" lang="plaintext">\-\-fastq_nostagger, \-\-fastq_qmax, \-\-fastq_qmin, and</span>
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1577
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<pre style="margin: 0;">+<span id="LC1577" class="line" lang="plaintext">\-\-label_suffix.</span>
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1552
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1578
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<pre style="margin: 0;"> <span id="LC1578" class="line" lang="plaintext">.TAG fastq_minlen</span>
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1553
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1579
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<pre style="margin: 0;"> <span id="LC1579" class="line" lang="plaintext">.TP</span>
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1554
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1580
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<pre style="margin: 0;"> <span id="LC1580" class="line" lang="plaintext">.BI \-\-fastq_minlen\~ "positive integer"</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">@@ -1580,10 +1606,11 @@ files. The default is 41, which is usual for recent Sanger/Illumina</td>
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1580
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1606
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<pre style="margin: 0;"> <span id="LC1606" class="line" lang="plaintext">.TAG fastq_qmaxout</span>
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1581
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1607
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<pre style="margin: 0;"> <span id="LC1607" class="line" lang="plaintext">.TP</span>
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1582
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1608
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<pre style="margin: 0;"> <span id="LC1608" class="line" lang="plaintext">.BI \-\-fastq_qmaxout\~ "positive integer"</span>
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1583
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<pre style="margin: 0;">-<span id="LC1583" class="line" lang="plaintext">When using \-\-fastq_convert or \-\-sff_convert, specify the maximum</span>
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1584
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<pre style="margin: 0;">-<span id="LC1584" class="line" lang="plaintext">quality score used when writing FASTQ files. The default is 41, which</span>
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1585
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<pre style="margin: 0;">-<span id="LC1585" class="line" lang="plaintext">is usual for recent Sanger/Illumina 1.8+ files. Older formats may use</span>
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1586
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<pre style="margin: 0;">-<span id="LC1586" class="line" lang="plaintext">a maximum quality score of 40.</span>
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1609
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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="plaintext">When using \-\-fastq_mergepairs, \-\-fastq_convert or \-\-sff_convert,</span>
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1610
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<pre style="margin: 0;">+<span id="LC1610" class="line" lang="plaintext">specify the maximum quality score used when writing FASTQ files. The</span>
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<pre style="margin: 0;">+<span id="LC1611" class="line" lang="plaintext">default is 41, which is usual for recent Sanger/Illumina 1.8+</span>
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<pre style="margin: 0;">+<span id="LC1612" class="line" lang="plaintext">files. Older formats may use a maximum quality score of 40. The limit</span>
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1613
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<pre style="margin: 0;">+<span id="LC1613" class="line" lang="plaintext">only applies to the merged region when using \-\-fastq_mergepairs.</span>
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1587
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1614
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<pre style="margin: 0;"> <span id="LC1614" class="line" lang="plaintext">.TAG fastq_qmin</span>
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1588
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1615
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<pre style="margin: 0;"> <span id="LC1615" class="line" lang="plaintext">.TP</span>
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1589
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1616
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<pre style="margin: 0;"> <span id="LC1616" class="line" lang="plaintext">.BI \-\-fastq_qmin\~ "positive integer"</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">@@ -1593,10 +1620,11 @@ files. Older formats may use scores between -5 and 2.</td>
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1593
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1620
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<pre style="margin: 0;"> <span id="LC1620" class="line" lang="plaintext">.TAG fastq_qminout</span>
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1594
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1621
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<pre style="margin: 0;"> <span id="LC1621" class="line" lang="plaintext">.TP</span>
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1595
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1622
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<pre style="margin: 0;"> <span id="LC1622" class="line" lang="plaintext">.BI \-\-fastq_qminout\~ "positive integer"</span>
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1596
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<pre style="margin: 0;">-<span id="LC1596" class="line" lang="plaintext">When using \-\-fastq_convert or \-\-sff_convert, specify the minimum</span>
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1597
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<pre style="margin: 0;">-<span id="LC1597" class="line" lang="plaintext">quality score used when writing FASTQ files. The default is 0, which</span>
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<td class="diff-line-num old old_line" data-linenumber="1598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1598
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<td class="diff-line-num new_line old" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1598" class="line" lang="plaintext">is usual for Sanger/Illumina 1.8+ files. Older versions of the format</span>
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1599
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<pre style="margin: 0;">-<span id="LC1599" class="line" lang="plaintext">may use scores between -5 and 2.</span>
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<pre style="margin: 0;">+<span id="LC1623" class="line" lang="plaintext">When using \-\-fastq_mergepairs, \-\-fastq_convert or \-\-sff_convert,</span>
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1624
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<pre style="margin: 0;">+<span id="LC1624" class="line" lang="plaintext">specify the minimum quality score used when writing FASTQ files. The</span>
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1625
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<pre style="margin: 0;">+<span id="LC1625" class="line" lang="plaintext">default is 0, which is usual for Sanger/Illumina 1.8+ files. Older</span>
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1626
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<pre style="margin: 0;">+<span id="LC1626" class="line" lang="plaintext">versions of the format may use scores between -5 and 2. The limit</span>
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<pre style="margin: 0;">+<span id="LC1627" class="line" lang="plaintext">applies only to the merged region when using \-\-fastq_mergepairs.</span>
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1600
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1628
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<pre style="margin: 0;"> <span id="LC1628" class="line" lang="plaintext">.TAG fastq_stats</span>
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1601
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1629
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<pre style="margin: 0;"> <span id="LC1629" class="line" lang="plaintext">.TP</span>
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1602
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1630
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<pre style="margin: 0;"> <span id="LC1630" class="line" lang="plaintext">.BI \-\-fastq_stats \0filename</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2411" style="width: 35px; color: rgba(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">@@ -2411,11 +2439,11 @@ Reject the sequence match if the alignment contains at least</td>
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2411
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2439
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<pre style="margin: 0;"> <span id="LC2439" class="line" lang="plaintext">\fIinteger\fR insertions or deletions.</span>
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2412
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2440
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<pre style="margin: 0;"> <span id="LC2440" class="line" lang="plaintext">.TAG maxhits</span>
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2413
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2441
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<pre style="margin: 0;"> <span id="LC2441" class="line" lang="plaintext">.TP</span>
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2414
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<pre style="margin: 0;">-<span id="LC2414" class="line" lang="plaintext">.BI \-\-maxhits\~ "<span class="idiff left right">posi</span>tive integer"</span>
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2442
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<pre style="margin: 0;">+<span id="LC2442" class="line" lang="plaintext">.BI \-\-maxhits\~ "<span class="idiff left right">non-nega</span>tive integer"</span>
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2415
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<td class="diff-line-num new_line" data-linenumber="2443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2443
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<pre style="margin: 0;"> <span id="LC2443" class="line" lang="plaintext">Maximum number of hits to show once the search is terminated (hits are</span>
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2416
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<pre style="margin: 0;">-<span id="LC2416" class="line" lang="plaintext">sorted by decreasing identity). Unlimited by default<span class="idiff left right">. That option</span></span>
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2417
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<pre style="margin: 0;">-<span id="LC2417" class="line" lang="plaintext">a<span class="idiff left right">pplies to \-\-alnout, \-\-blast6out, \-\-fastapairs, \-\-sam</span>out,</span>
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2418
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<pre style="margin: 0;">-<span id="LC2418" class="line" lang="plaintext">\-\-uc, or \-\-userout output files.</span>
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2444
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<pre style="margin: 0;">+<span id="LC2444" class="line" lang="plaintext">sorted by decreasing identity). Unlimited by default<span class="idiff left right"> or if the</span></span>
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2445
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<pre style="margin: 0;">+<span id="LC2445" class="line" lang="plaintext">a<span class="idiff left right">rgument it zero. This option applies to \-\-alnout, \-\-blast6</span>out,</span>
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2446
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<pre style="margin: 0;">+<span id="LC2446" class="line" lang="plaintext">\-\-<span class="idiff left right">fastapairs, \-\-samout, \-\-</span>uc, or \-\-userout output files.</span>
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2419
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2447
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<pre style="margin: 0;"> <span id="LC2447" class="line" lang="plaintext">.TAG maxid</span>
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2420
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2448
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<pre style="margin: 0;"> <span id="LC2448" class="line" lang="plaintext">.TP</span>
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2421
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2449
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<pre style="margin: 0;"> <span id="LC2449" class="line" lang="plaintext">.BI \-\-maxid \0real</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3099" style="width: 35px; color: rgba(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="3127" style="width: 35px; color: rgba(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">@@ -3099,6 +3127,9 @@ rank. Commas and semicolons are not allowed in the name of the rank.</td>
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3099
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3127
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<pre style="margin: 0;"> <span id="LC3127" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num old_line" data-linenumber="3100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3100
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<td class="diff-line-num new_line" data-linenumber="3128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3128
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<pre style="margin: 0;"> <span id="LC3128" class="line" lang="plaintext">Example: ">X80725_S000004313;\:tax=d:Bacteria,\:p:Proteobacteria,\:c:Gammaproteobacteria,\:o:Enterobacteriales,\:f:Enterobacteriaceae,\:g:Escherichia/Shigella,\:s:Escherichia_coli".</span>
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3101
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3129
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<pre style="margin: 0;"> <span id="LC3129" class="line" lang="plaintext">.PP</span>
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3130
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<pre style="margin: 0;">+<span id="LC3130" class="line" lang="plaintext">The option \-\-notrunclabels is turned on by default for this command,</span>
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3131
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<pre style="margin: 0;">+<span id="LC3131" class="line" lang="plaintext">allowing spaces in the taxonomic identifiers.</span>
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3132
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<pre style="margin: 0;">+<span id="LC3132" class="line" lang="plaintext">.PP</span>
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3102
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3133
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<pre style="margin: 0;"> <span id="LC3133" class="line" lang="plaintext">.TAG db</span>
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3103
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3134
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<pre style="margin: 0;"> <span id="LC3134" class="line" lang="plaintext">.TP 9</span>
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3104
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3135
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<pre style="margin: 0;"> <span id="LC3135" class="line" lang="plaintext">.BI \-\-db \0filename</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3422" style="width: 35px; color: rgba(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">@@ -3391,8 +3422,8 @@ field is set to 0 if there is no alignment.</td>
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3391
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3422
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<pre style="margin: 0;"> <span id="LC3422" class="line" lang="plaintext">.TP</span>
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3392
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3423
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<pre style="margin: 0;"> <span id="LC3423" class="line" lang="plaintext">.B tstrand</span>
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3393
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3424
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<pre style="margin: 0;"> <span id="LC3424" class="line" lang="plaintext">Target strand orientation (+ or - for nucleotide sequences). Always</span>
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3394
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<pre style="margin: 0;">-<span id="LC3394" class="line" lang="plaintext">set to '+', so reverse strand matches have tstrand '+' and<span class="idiff left right"> qstrand</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3395
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<td class="diff-line-num new_line old" data-linenumber="3425" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3395" class="line" lang="plaintext"><span class="idiff left right">'</span>-'. Empty field if there is no alignment.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3425
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<pre style="margin: 0;">+<span id="LC3425" class="line" lang="plaintext">set to '+', so reverse strand matches have tstrand '+' and</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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="plaintext"><span class="idiff left right">qstrand '\</span>-'. Empty field if there is no alignment.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3396
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<td class="diff-line-num new_line" data-linenumber="3427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3427
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<pre style="margin: 0;"> <span id="LC3427" class="line" lang="plaintext">.RE</span>
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<td class="diff-line-num old_line" data-linenumber="3397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3397
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<td class="diff-line-num new_line" data-linenumber="3428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3428
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<pre style="margin: 0;"> <span id="LC3428" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num 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">
3398
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<td class="diff-line-num new_line" data-linenumber="3429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3429
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<pre style="margin: 0;"> <span id="LC3429" class="line" lang="plaintext">.\" ============================================================================</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4240" style="width: 35px; color: rgba(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="4271" style="width: 35px; color: rgba(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">@@ -4240,9 +4271,20 @@ relabelling options valid for certain commands.</td>
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<td class="diff-line-num old_line" data-linenumber="4240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4240
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<td class="diff-line-num new_line" data-linenumber="4271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4271
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<pre style="margin: 0;"> <span id="LC4271" class="line" lang="plaintext">Fixed bug with sequences written to file specified with fastaout_rev</span>
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<td class="diff-line-num old_line" data-linenumber="4241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4241
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<td class="diff-line-num new_line" data-linenumber="4272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4272
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4272" class="line" lang="plaintext">for commands fastx_filter and fastq_filter.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4242
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<td class="diff-line-num new_line" data-linenumber="4273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4273
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4273" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4243
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<td class="diff-line-num new_line old" data-linenumber="4274" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC4243" class="line" lang="plaintext">.BR v2.14.2\~ "released January 28th, 2020<span class="idiff left right">2</span>"</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4274
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<pre style="margin: 0;">+<span id="LC4274" class="line" lang="plaintext">.BR v2.14.2\~ "released January 28th, 2020"</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="4244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4244
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<td class="diff-line-num new_line" data-linenumber="4275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4275
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<pre style="margin: 0;"> <span id="LC4275" class="line" lang="plaintext">Fixed some issues with the cut, fastx_revcomp, fastq_convert,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4245
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<td class="diff-line-num new_line" data-linenumber="4276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4276
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4276" class="line" lang="plaintext">fastq_mergepairs, and makeudb_usearch commands. Updated manual.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4277
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<pre style="margin: 0;">+<span id="LC4277" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4278
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<pre style="margin: 0;">+<span id="LC4278" class="line" lang="plaintext">.BR v2.15.0\~ "released June 19th, 2020"</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4279
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<pre style="margin: 0;">+<span id="LC4279" class="line" lang="plaintext">Update manual and documentation. Turn on notrunclabels option for</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4280
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<pre style="margin: 0;">+<span id="LC4280" class="line" lang="plaintext">sintax command by default. Change maxhits 0 to mean unlimited hits,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4281
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<pre style="margin: 0;">+<span id="LC4281" class="line" lang="plaintext">like the default. Allow non-ascii characters in headers, with a</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4282
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<pre style="margin: 0;">+<span id="LC4282" class="line" lang="plaintext">warning. Sort centroids and uc too when clusterout_sort specified. Add</span>
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<td class="diff-line-num new new_line" data-linenumber="4283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4283
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<pre style="margin: 0;">+<span id="LC4283" class="line" lang="plaintext">cluster id to centroids output when clusterout_id specified. Improve</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4284
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<pre style="margin: 0;">+<span id="LC4284" class="line" lang="plaintext">error messages when parsing FASTQ files. Add missing fastq_qminout</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4285
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<pre style="margin: 0;">+<span id="LC4285" class="line" lang="plaintext">option and fix label_suffix option for fastq_mergepairs. Add derep_id</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4286
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<pre style="margin: 0;">+<span id="LC4286" class="line" lang="plaintext">command that dereplicates based on both label and sequence. Remove</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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4287
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<pre style="margin: 0;">+<span id="LC4287" class="line" lang="plaintext">compilation warnings.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4246
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<td class="diff-line-num new_line" data-linenumber="4288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4288
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<pre style="margin: 0;"> <span id="LC4288" class="line" lang="plaintext">.LP</span>
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<pre style="margin: 0;"> <span id="LC4289" class="line" lang="plaintext">.\" ============================================================================</span>
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<pre style="margin: 0;"> <span id="LC4290" class="line" lang="plaintext">.\" TODO:</span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#d79e6705e3db119ee1bb6ad9670fe99b162c13b0"><strong>src/cluster.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">@@ -1197,12 +1197,17 @@ void cluster(char * dbname,</td>
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<pre style="margin: 0;"> <span id="LC1197" class="line" lang="cpp"> <span class="p">}</span></span>
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1198
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<pre style="margin: 0;"> <span id="LC1198" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1199" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1200" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* Sort <span class="idiff left right">clusters</span> */</span></span>
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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* Sort <span class="idiff left right">sequences in clusters by their abundance or ordinal number</span> */</span></span>
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1201
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<pre style="margin: 0;"> <span id="LC1201" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* Sequences in same cluster must always come right after each other. */</span></span>
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1202
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1202
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* The centroid sequence must be the first in each cluster. */</span></span>
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1203
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1203
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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="cpp"></span>
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1204
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1204
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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_init</span><span class="p">(</span><span class="s" style="color: #d14;">"Sorting clusters"</span><span class="p">,</span> <span class="n" style="color: #333;">clusters</span><span class="p">);</span></span>
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1205
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<pre style="margin: 0;">-<span id="LC1205" class="line" lang="cpp"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">clusterinfo</span><span class="p">,</span> <span class="n" style="color: #333;">seqcount</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">clusterinfo_t</span><span class="p">),</span> <span class="n" style="color: #333;">compare_byclusterno</span><span class="p">);</span></span>
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1205
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_clusterout_sort</span><span class="p">)</span></span>
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1206
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<pre style="margin: 0;">+<span id="LC1206" class="line" lang="cpp"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">clusterinfo</span><span class="p">,</span> <span class="n" style="color: #333;">seqcount</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">clusterinfo_t</span><span class="p">),</span></span>
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1207
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="cpp"> <span class="n" style="color: #333;">compare_byclusterabundance</span><span class="p">);</span></span>
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1208
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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1209
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="cpp"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">clusterinfo</span><span class="p">,</span> <span class="n" style="color: #333;">seqcount</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">clusterinfo_t</span><span class="p">),</span></span>
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1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="cpp"> <span class="n" style="color: #333;">compare_byclusterno</span><span class="p">);</span></span>
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1206
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1211
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<pre style="margin: 0;"> <span id="LC1211" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_done</span><span class="p">();</span></span>
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1207
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1212
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<pre style="margin: 0;"> <span id="LC1212" class="line" lang="cpp"></span>
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1208
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1213
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<pre style="margin: 0;"> <span id="LC1213" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_init</span><span class="p">(</span><span class="s" style="color: #d14;">"Writing clusters"</span><span class="p">,</span> <span class="n" style="color: #333;">seqcount</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1237" style="width: 35px; color: rgba(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="1242" style="width: 35px; color: rgba(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">@@ -1237,7 +1242,9 @@ void cluster(char * dbname,</td>
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<pre style="margin: 0;"> <span id="LC1242" class="line" lang="cpp"> <span class="n" style="color: #333;">cluster_abundance</span><span class="p">[</span><span class="n" style="color: #333;">clusterno</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC1243" class="line" lang="cpp"> <span class="n" style="color: #333;">clusterno</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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1244
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<pre style="margin: 0;"> <span id="LC1244" 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="LC1240" 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 class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1245" 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="LC1246" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_clusterout_id</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">clusterno</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</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="LC1248" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_uc</span><span class="p">)</span></span>
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1250
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<pre style="margin: 0;"> <span id="LC1250" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp_uc</span><span class="p">,</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;">%"</span> <span class="n" style="color: #333;">PRId64</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</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="diff-line-num unfold js-unfold old_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>
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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">@@ -1332,15 +1339,6 @@ void cluster(char * dbname,</td>
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<pre style="margin: 0;"> <span id="LC1339" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1340" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1341" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1335" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_clusterout_sort</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1336" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1337" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* Optionally sort clusters by abundance */</span></span>
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<pre style="margin: 0;">-<span id="LC1338" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_init</span><span class="p">(</span><span class="s" style="color: #d14;">"Sorting clusters by abundance"</span><span class="p">,</span> <span class="n" style="color: #333;">clusters</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1339" class="line" lang="cpp"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">clusterinfo</span><span class="p">,</span> <span class="n" style="color: #333;">seqcount</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">clusterinfo_t</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC1340" class="line" lang="cpp"> <span class="n" style="color: #333;">compare_byclusterabundance</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1341" 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="LC1342" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1343" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_msaout</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_consout</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_profile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">msa_target_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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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#e0f36bd5084cd7076742276f78c5e2d9d62127df"><strong>src/derep.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">@@ -204,9 +204,10 @@ void rehash(struct bucket * * hashtableref, int64_t alloc_clusters)</td>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hashtableref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_hashtable</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">derep_fulllength</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">derep</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">input_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">use_header</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* dereplicate full length sequences, optionally require identical headers */</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">show_rusage</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC213" 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_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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<td class="diff-line-num unfold js-unfold old_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>
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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">@@ -226,7 +227,7 @@ void derep_fulllength()</td>
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<pre style="margin: 0;"> <span id="LC227" 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 output (uc) file for writing"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC229" 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;"><span class="idiff left right">opt_derep_fulllength</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC230" 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;"><span class="idiff left right">input_filename</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">show_rusage</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="282" style="width: 35px; color: rgba(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">@@ -281,7 +282,7 @@ void derep_fulllength()</td>
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<pre style="margin: 0;"> <span id="LC282" 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;">rc_seq_up</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;">xmalloc</span><span class="p">(</span><span class="n" style="color: #333;">alloc_seqlen</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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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"></span>
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284
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<pre style="margin: 0;"> <span id="LC284" 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;">prompt</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xsprintf</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">prompt</span><span class="p">,</span> <span class="s" style="color: #d14;">"Dereplicating file %s"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">opt_derep_fulllength</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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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;">xsprintf</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">prompt</span><span class="p">,</span> <span class="s" style="color: #d14;">"Dereplicating file %s"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">input_filename</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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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;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Out of memory"</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>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_init</span><span class="p">(</span><span class="n" style="color: #333;">prompt</span><span class="p">,</span> <span class="n" style="color: #333;">filesize</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">@@ -368,6 +369,8 @@ void derep_fulllength()</td>
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368
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="cpp"> <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="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq</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;">h</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC372" 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;">header</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;">h</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">headerlen</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;">h</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* normalize sequence: uppercase and replace U by T */</span></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp"> <span class="n" style="color: #333;">string_normalize</span><span class="p">(</span><span class="n" style="color: #333;">seq_up</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="385" style="width: 35px; color: rgba(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="388" style="width: 35px; color: rgba(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">@@ -385,13 +388,16 @@ void derep_fulllength()</td>
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385
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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386
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp"></span>
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387
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HASH</span><span class="p">(</span><span class="n" style="color: #333;">seq_up</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">use_header</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">^=</span> <span class="n" style="color: #333;">HASH</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">headerlen</span><span class="p">);</span></span>
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388
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">hash_mask</span><span class="p">;</span></span>
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389
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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;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">bucket</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashtable</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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390
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="cpp"></span>
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391
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">)</span></span>
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392
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span></span>
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393
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp"> <span class="p">((</span><span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hash</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">seqcmp</span><span class="p">(</span><span class="n" style="color: #333;">seq_up</span><span class="p">,</span> <span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</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 class="n" style="color: #333;">seqcmp</span><span class="p">(</span><span class="n" style="color: #333;">seq_up</span><span class="p">,</span> <span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">use_header</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">header</span><span class="p">))))</span></span>
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395
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp"> <span class="p">{</span></span>
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396
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">j</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;">hash_mask</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
397
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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;">bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashtable</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="409" style="width: 35px; color: rgba(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="415" style="width: 35px; color: rgba(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">@@ -409,7 +415,8 @@ void derep_fulllength()</td>
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409
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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;">while</span> <span class="p">((</span><span class="n" style="color: #333;">rc_bp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">)</span></span>
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410
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416
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span></span>
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411
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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 class="n" style="color: #333;">rc_hash</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">rc_bp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hash</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">seqcmp</span><span class="p">(</span><span class="n" style="color: #333;">rc_seq_up</span><span class="p">,</span> <span class="n" style="color: #333;">rc_bp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><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="p">(</span><span class="n" style="color: #333;">seqcmp</span><span class="p">(</span><span class="n" style="color: #333;">rc_seq_up</span><span class="p">,</span> <span class="n" style="color: #333;">rc_bp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">use_header</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">bp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">header</span><span class="p">))))</span></span>
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413
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"> <span class="p">{</span></span>
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414
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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;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">k</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;">hash_mask</span><span class="p">;</span></span>
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415
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422
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="cpp"> <span class="n" style="color: #333;">rc_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashtable</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="424" style="width: 35px; color: rgba(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="431" style="width: 35px; color: rgba(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">@@ -424,7 +431,6 @@ void derep_fulllength()</td>
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424
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431
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> <span class="p">}</span></span>
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425
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432
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"> <span class="p">}</span></span>
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426
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433
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp"></span>
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427
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<pre style="margin: 0;">-<span id="LC427" 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;">header</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;">h</span><span class="p">);</span></span>
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428
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434
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">abundance</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;">h</span><span class="p">);</span></span>
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429
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435
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">ab</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_sizein</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">abundance</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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430
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436
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="cpp"> <span class="n" style="color: #333;">sumsize</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ab</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1086" style="width: 35px; color: rgba(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="1092" style="width: 35px; color: rgba(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">@@ -1086,3 +1092,13 @@ void derep_prefix()</td>
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1086
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1092
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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">hashtable</span><span class="p">);</span></span>
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1087
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1093
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<pre style="margin: 0;"> <span id="LC1093" class="line" lang="cpp"> <span class="n" style="color: #333;">db_free</span><span class="p">();</span></span>
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1088
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1094
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<pre style="margin: 0;"> <span id="LC1094" class="line" lang="cpp"><span class="p">}</span></span>
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1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="cpp"></span>
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1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">derep_fulllength</span><span class="p">()</span></span>
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1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="cpp"><span class="p">{</span></span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="cpp"> <span class="n" style="color: #333;">derep</span><span class="p">(</span><span class="n" style="color: #333;">opt_derep_fulllength</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="cpp"><span class="p">}</span></span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">derep_id</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="cpp"><span class="p">{</span></span>
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1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="cpp"> <span class="n" style="color: #333;">derep</span><span class="p">(</span><span class="n" style="color: #333;">opt_derep_id</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#8f8dff040d7feb7206c5df2f516c3df968e7268b"><strong>src/derep.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">@@ -59,4 +59,5 @@</td>
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59
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59
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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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60
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"></span>
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61
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61
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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;">derep_fulllength</span><span class="p">();</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">derep_id</span><span class="p">();</span></span>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">derep_prefix</span><span class="p">();</span></span></pre>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#67ef99e491c4bda5d0c47f152cae53d18d7fbcd3"><strong>src/fasta.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">@@ -366,6 +366,9 @@ void fasta_print_general(FILE * fp,</td>
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="cpp"> <span class="n" style="color: #333;">xee</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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368
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="cpp"></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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_label_suffix</span><span class="p">)</span></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;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">opt_label_suffix</span><span class="p">);</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"></span>
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369
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">clustersize</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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370
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373
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<pre style="margin: 0;"> <span id="LC373" 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;">";seqs=%d"</span><span class="p">,</span> <span class="n" style="color: #333;">clustersize</span><span class="p">);</span></span>
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371
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#d6ab431461af8e07f1ea378788017353266e8ba2"><strong>src/fastq.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">@@ -84,19 +84,18 @@ void buffer_filter_extend(fastx_handle h,</td>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC85" 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;">char_action</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC86" 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;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">char_mapping</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">lineno_start</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ok</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC88" 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;">illegal_char</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer_makespace</span><span class="p">(</span><span class="n" style="color: #333;">dest_buffer</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* Strip unwanted characters from the string and raise warnings or</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> errors on certain characters. */</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">lineno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lineno_start</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>
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<pre style="margin: 0;"> <span id="LC95" 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;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">source_buf</span><span class="p">;</span></span>
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97
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96
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<pre style="margin: 0;"> <span id="LC96" 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;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dest_buffer</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dest_buffer</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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98
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97
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<pre style="margin: 0;"> <span id="LC97" 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;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">msg</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">200</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ok</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">true</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"></span>
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101
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<pre style="margin: 0;"> <span id="LC100" 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;">uint64_t</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;">len</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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102
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<pre style="margin: 0;"> <span id="LC101" 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="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,17 +117,9 @@ void buffer_filter_extend(fastx_handle h,</td>
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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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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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120
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* fatal character */</span></span>
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<pre style="margin: 0;">-<span id="LC121" 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="mi" style="color: #099;">32</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="mi" style="color: #099;">127</span><span class="p">))</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp"> <span class="mi" style="color: #099;">200</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Illegal character '%c'"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC125" 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="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp"> <span class="mi" style="color: #099;">200</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Illegal unprintable ASCII character no %d"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</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="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">fastq_fatal</span><span class="p">(</span><span class="n" style="color: #333;">lineno</span><span class="p">,</span> <span class="n" style="color: #333;">msg</span><span class="p">);</span></span>
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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;">ok</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">illegal_char</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC123" 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="LC124" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -137,7 +128,6 @@ void buffer_filter_extend(fastx_handle h,</td>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">4</span><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="cm" style="color: #998; font-style: italic;">/* newline (silently stripped) */</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">lineno</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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141
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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;">break</span><span class="p">;</span></span>
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142
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="p">}</span></span>
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143
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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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="177" style="width: 35px; color: rgba(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="167" style="width: 35px; color: rgba(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">@@ -177,6 +167,10 @@ bool fastq_next(fastx_handle h,</td>
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177
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"></span>
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178
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168
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<pre style="margin: 0;"> <span id="LC168" 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;">lineno_start</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;">lineno</span><span class="p">;</span></span>
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179
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">msg</span><span class="p">[</span><span class="mi" style="color: #099;">200</span><span class="p">];</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</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 class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">illegal_char</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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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"></span>
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180
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<pre style="margin: 0;"> <span id="LC174" 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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181
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"></span>
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182
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* check end of file */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="221" style="width: 35px; color: rgba(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="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -221,8 +215,6 @@ bool fastq_next(fastx_handle h,</td>
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221
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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222
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"> <span class="p">}</span></span>
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223
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"></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;">uint64_t</span> <span class="n" style="color: #333;">lineno_seq</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;">lineno</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="LC218" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* read sequence line(s) */</span></span>
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227
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">lf</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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228
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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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">@@ -255,17 +247,26 @@ bool fastq_next(fastx_handle h,</td>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"> <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;">sequence_buffer</span><span class="p">,</span></span>
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256
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248
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<pre style="margin: 0;"> <span id="LC248" 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;">file_buffer</span><span class="p">.</span><span class="n" style="color: #333;">data</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;">position</span><span class="p">,</span></span>
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257
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">len</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="n" style="color: #333;">char_fq_action_seq</span><span class="p">,</span> <span class="n" style="color: #333;">char_mapping</span><span class="p">,</span> <span class="n" style="color: #333;">lineno_seq</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;">char_fq_action_seq</span><span class="p">,</span> <span class="n" style="color: #333;">char_mapping</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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ok</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">illegal_char</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;">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;">position</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"> <span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if (h->sequence_buffer.length == 0)</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> fastq_fatal(lineno_seq, "Empty sequence line");</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">lineno_plus</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;">lineno</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC255" 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;">ok</span><span class="p">)</span></span>
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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="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">illegal_char</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">illegal_char</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">127</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="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">msg</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="mi" style="color: #099;">200</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Illegal sequence character '%c'"</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="n" style="color: #333;">illegal_char</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="k" style="font-weight: 600;">else</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="mi" style="color: #099;">200</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="s" style="color: #d14;">"Illegal sequence character (unprintable, no %d)"</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span> <span class="n" style="color: #333;">illegal_char</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 class="n" style="color: #333;">fastq_fatal</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;">lineno</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">lf</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="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">msg</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="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="p">}</span></span>
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269
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp"></span>
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* read + line */</span></span>
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271
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="319" style="width: 35px; color: rgba(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">@@ -319,13 +320,11 @@ bool fastq_next(fastx_handle h,</td>
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319
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">plusline_invalid</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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320
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"> <span class="p">}</span></span>
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321
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">plusline_invalid</span><span class="p">)</span></span>
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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">fastq_fatal</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">lineno_plus</span></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="n" style="color: #333;">fastq_fatal</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">h</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">lineno</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lf</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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323
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"> <span class="s" style="color: #d14;">"'+' line must be empty or identical to header"</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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325
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* read quality line(s) */</span></span>
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">lineno_qual</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;">lineno</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"> <span class="n" style="color: #333;">lf</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="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC330" 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">@@ -354,22 +353,38 @@ bool fastq_next(fastx_handle h,</td>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lf</span> <span class="o" style="font-weight: 600;">-</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;">file_buffer</span><span class="p">.</span><span class="n" style="color: #333;">data</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;">position</span><span class="p">)</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="LC354" 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;">lineno</span><span class="o" style="font-weight: 600;">++</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>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer_filter_extend</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="LC358" class="line" lang="cpp"> <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;">quality_buffer</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;">file_buffer</span><span class="p">.</span><span class="n" style="color: #333;">data</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;">position</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;">len</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">char_fq_action_qual</span><span class="p">,</span> <span class="n" style="color: #333;">chrmap_identity</span><span class="p">,</span> <span class="n" style="color: #333;">lineno_qual</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">char_fq_action_qual</span><span class="p">,</span> <span class="n" style="color: #333;">chrmap_identity</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ok</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">illegal_char</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC363" 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;">file_buffer</span><span class="p">.</span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="cpp"> <span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC364" 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>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> if (h->quality_buffer.length == 0)</span></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> fastq_fatal(lineno_seq, "Empty quality line");</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* break if quality line already too long */</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" 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;">quality_buffer</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequence_buffer</span><span class="p">.</span><span class="n" style="color: #333;">length</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="k" style="font-weight: 600;">break</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>
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370
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<pre style="margin: 0;">+<span id="LC370" 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;">ok</span><span class="p">)</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <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="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">illegal_char</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">illegal_char</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">127</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="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="mi" style="color: #099;">200</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="s" style="color: #d14;">"Illegal quality character '%c'"</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="n" style="color: #333;">illegal_char</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="k" style="font-weight: 600;">else</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="mi" style="color: #099;">200</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="s" style="color: #d14;">"Illegal quality character (unprintable, no %d)"</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span> <span class="n" style="color: #333;">illegal_char</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;">fastq_fatal</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;">lineno</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">lf</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="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">msg</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 class="p">}</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" 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>
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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;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequence_buffer</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quality_buffer</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="cpp"> <span class="n" style="color: #333;">fastq_fatal</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">lineno_qual</span></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;">fastq_fatal</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">h</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">lineno</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lf</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Sequence and quality lines must be equally long"</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>
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp"> <span class="n" style="color: #333;">fastx_filter_header</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">truncateatspace</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="498" style="width: 35px; color: rgba(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">@@ -483,6 +498,9 @@ void fastq_print_general(FILE * fp,</td>
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="cpp"> <span class="n" style="color: #333;">xee</span><span class="p">);</span></span>
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="cpp"> <span class="p">}</span></span>
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485
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500
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="cpp"></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_label_suffix</span><span class="p">)</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" 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;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">opt_label_suffix</span><span class="p">);</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp"></span>
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504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_sizeout</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">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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487
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505
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<pre style="margin: 0;"> <span id="LC505" 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;">";size=%u"</span><span class="p">,</span> <span class="n" style="color: #333;">abundance</span><span class="p">);</span></span>
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488
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506
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#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">@@ -653,11 +653,6 @@ void fastx_revcomp()</td>
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653
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653
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<pre style="margin: 0;"> <span id="LC653" 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;">seq_buffer</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;">xmalloc</span><span class="p">(</span><span class="n" style="color: #333;">buffer_alloc</span><span class="p">);</span></span>
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654
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<pre style="margin: 0;"> <span id="LC654" 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;">qual_buffer</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;">xmalloc</span><span class="p">(</span><span class="n" style="color: #333;">buffer_alloc</span><span class="p">);</span></span>
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655
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">header_alloc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">512</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC657" 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;">header</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;">xmalloc</span><span class="p">(</span><span class="n" style="color: #333;">header_alloc</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">suffix_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_label_suffix</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">opt_label_suffix</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="LC660" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC656" 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;">opt_fastx_revcomp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC658" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -699,22 +694,7 @@ void fastx_revcomp()</td>
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* header */</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="LC696" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">hlen</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;">h</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hlen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_length</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;">header_alloc</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="cpp"> <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;">header_alloc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hlen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_length</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="LC706" class="line" lang="cpp"> <span class="n" style="color: #333;">header</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;">header</span><span class="p">,</span> <span class="n" style="color: #333;">header_alloc</span><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="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">d</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;">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="n" style="color: #333;">opt_label_suffix</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;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">header_alloc</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s%s"</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">opt_label_suffix</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;">else</span></span>
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">header_alloc</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="cpp"> <span class="n" style="color: #333;">hlen</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">suffix_length</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC697" 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;">header</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;">h</span><span class="p">);</span></span>
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718
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698
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">abundance</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;">h</span><span class="p">);</span></span>
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719
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699
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="cpp"></span>
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720
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700
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="780" style="width: 35px; color: rgba(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="760" style="width: 35px; color: rgba(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">@@ -780,7 +760,6 @@ void fastx_revcomp()</td>
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780
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="cpp"></span>
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781
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="cpp"> <span class="n" style="color: #333;">fastx_close</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">);</span></span>
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782
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC783" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">);</span></span>
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784
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763
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">seq_buffer</span><span class="p">);</span></span>
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">qual_buffer</span><span class="p">);</span></span>
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786
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="cpp"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#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">@@ -169,6 +169,28 @@ void fastx_filter_header(fastx_handle h, bool truncateatspace)</td>
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169
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"></span>
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170
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>
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171
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">7</span><span class="p">:</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* Non-ASCII but acceptable */</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" 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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175
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<pre style="margin: 0;">+<span id="LC175" 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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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="s" style="color: #d14;">"WARNING: Non-ASCII character encountered in FASTA/FASTQ header.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Character no %d (0x%2x) on or right before line %"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <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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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineno</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>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fp_log</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="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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184
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<pre style="margin: 0;">+<span id="LC184" 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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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"> <span class="s" style="color: #d14;">"WARNING: Non-ASCII character encountered in FASTA/FASTQ header.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Character no %d (0x%2x) on or right before line %"</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <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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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">c</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="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineno</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>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</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="k" style="font-weight: 600;">break</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>
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172
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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;">case</span> <span class="mi" style="color: #099;">5</span><span class="p">:</span></span>
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173
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<td class="diff-line-num new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">6</span><span class="p">:</span></span>
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174
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* tab or space */</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#5d506abf37fc32f1877a3abd29631760d6209ba5"><strong>src/maps.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">@@ -84,6 +84,7 @@ unsigned int char_header_action[256] =</td>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> 4 = lf</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> 5 = tab</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> 6 = space</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> 7 = non-ascii, legal, but warn</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> @ A B C D E F G H I J K L M N O</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> P Q R S T U V W X Y Z [ \ ] ^ _</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">@@ -97,14 +98,14 @@ unsigned int char_header_action[256] =</td>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <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 class="mi" style="color: #099;">1</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 class="mi" style="color: #099;">1</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 class="mi" style="color: #099;">1</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 class="mi" style="color: #099;">1</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 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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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <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 class="mi" style="color: #099;">1</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 class="mi" style="color: #099;">1</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 class="mi" style="color: #099;">1</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 class="mi" style="color: #099;">1</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 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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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <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 class="mi" style="color: #099;">1</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 class="mi" style="color: #099;">1</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 class="mi" style="color: #099;">1</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 class="mi" style="color: #099;">1</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 class="mi" style="color: #099;">1</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="LC100" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">,</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">,</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">,</span></span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">7</span></span><span class="p">,</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">7</span></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="mi" style="color: #099;"><span class="idiff left">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">7</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">7</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">7</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">7</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">7</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">7</span></span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="p">};</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="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;">char_fasta_action</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#9c689a31237f70b17e9bac31f42d1b22ea1d59be"><strong>src/mergepairs.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -188,11 +188,9 @@ typedef struct merge_data_s</td>
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188
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">fwd_trunc</span><span class="p">;</span></span>
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189
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">rev_trunc</span><span class="p">;</span></span>
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190
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">pair_no</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="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">merged_header</span><span class="p">;</span></span>
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192
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191
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<pre style="margin: 0;"> <span id="LC191" 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;">merged_sequence</span><span class="p">;</span></span>
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193
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192
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<pre style="margin: 0;"> <span id="LC192" 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;">merged_quality</span><span class="p">;</span></span>
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194
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">merged_length</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="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">merged_header_alloc</span><span class="p">;</span></span>
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196
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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;">int64_t</span> <span class="n" style="color: #333;">merged_seq_alloc</span><span class="p">;</span></span>
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197
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ee_merged</span><span class="p">;</span></span>
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198
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ee_fwd</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -310,13 +308,17 @@ void precompute_qual()</td>
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cpp"></span>
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* Match */</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">px</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">py</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">3.0</span> <span class="o" style="font-weight: 600;">/</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;">px</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">py</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">4.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">px</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">py</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">3.0</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;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_fastq_ascii</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">round</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">10.0</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">log10</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)),</span> <span class="n" style="color: #333;">opt_fastq_qmaxout</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">merge_qual_same</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">][</span><span class="n" style="color: #333;">y</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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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;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">round</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">10.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">log10</span><span class="p">(</span><span class="n" style="color: #333;">p</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;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">opt_fastq_qmaxout</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;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">opt_fastq_qminout</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">merge_qual_same</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">][</span><span class="n" style="color: #333;">y</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_fastq_ascii</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* Mismatch, x is highest quality */</span></span>
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317
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">px</span> <span class="o" style="font-weight: 600;">*</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;">py</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">3.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">px</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">py</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">4.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">px</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">py</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">3.0</span><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="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_fastq_ascii</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">round</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">10.0</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">log10</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)),</span> <span class="n" style="color: #333;">opt_fastq_qmaxout</span><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="n" style="color: #333;">merge_qual_diff</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">][</span><span class="n" style="color: #333;">y</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">round</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">10.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">log10</span><span class="p">(</span><span class="n" style="color: #333;">p</span><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="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">opt_fastq_qmaxout</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;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">opt_fastq_qminout</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="n" style="color: #333;">merge_qual_diff</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">][</span><span class="n" style="color: #333;">y</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_fastq_ascii</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> observed match,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="392" style="width: 35px; color: rgba(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="394" style="width: 35px; color: rgba(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">@@ -392,8 +394,8 @@ void keep(merge_data_t * ip)</td>
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392
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394
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<pre style="margin: 0;"> <span id="LC394" 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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393
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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;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_sequence</span><span class="p">,</span></span>
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394
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_length</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;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">merge</span>d_header</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="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">merge</span>d_header</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="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">fw</span>d_header</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;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">fw</span>d_header</span><span class="p">),</span></span>
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397
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_quality</span><span class="p">,</span></span>
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398
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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399
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp"> <span class="n" style="color: #333;">merged</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="406" style="width: 35px; color: rgba(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="408" style="width: 35px; color: rgba(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">@@ -406,8 +408,8 @@ void keep(merge_data_t * ip)</td>
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406
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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407
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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;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_sequence</span><span class="p">,</span></span>
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408
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_length</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;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">merge</span>d_header</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="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">merge</span>d_header</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">fw</span>d_header</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">fw</span>d_header</span><span class="p">),</span></span>
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411
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</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="n" style="color: #333;">merged</span><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="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ee_merged</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">@@ -645,12 +647,6 @@ void merge(merge_data_t * ip)</td>
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647
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ee_merged</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">opt_fastq_maxee</span><span class="p">)</span></span>
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649
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<pre style="margin: 0;"> <span id="LC649" 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 class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_label_suffix</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="cpp"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_header</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s%s"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fwd_header</span><span class="p">,</span> <span class="n" style="color: #333;">opt_label_suffix</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_header</span><span class="p">,</span> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fwd_header</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="cpp"></span>
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650
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">reason</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ok</span><span class="p">;</span></span>
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655
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<td class="diff-line-num new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
651
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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656
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652
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<pre style="margin: 0;"> <span id="LC652" 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="932" style="width: 35px; color: rgba(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="928" style="width: 35px; color: rgba(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">@@ -932,8 +928,6 @@ void process(merge_data_t * ip,</td>
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932
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928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="cpp"></span>
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933
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<td class="diff-line-num new_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">read_pair</span><span class="p">(</span><span class="n" style="color: #333;">merge_data_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ip</span><span class="p">)</span></span>
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934
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930
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
935
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<td class="diff-line-num new_line old" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC935" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">suffix_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_label_suffix</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">opt_label_suffix</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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<td class="diff-line-num old old_line" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
936
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<td class="diff-line-num new_line old" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC936" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
937
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastq_next</span><span class="p">(</span><span class="n" style="color: #333;">fastq_fwd</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">chrmap_upcase</span><span class="p">))</span></span>
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<td class="diff-line-num old_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
938
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932
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<pre style="margin: 0;"> <span id="LC932" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
939
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933
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<pre style="margin: 0;"> <span id="LC933" 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_next</span><span class="p">(</span><span class="n" style="color: #333;">fastq_rev</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">chrmap_upcase</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="979" style="width: 35px; color: rgba(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="973" style="width: 35px; color: rgba(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">@@ -979,15 +973,6 @@ bool read_pair(merge_data_t * ip)</td>
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979
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973
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<pre style="margin: 0;"> <span id="LC973" class="line" lang="cpp"> <span class="n" style="color: #333;">merged_seq_needed</span><span class="p">);</span></span>
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980
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974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
981
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975
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<pre style="margin: 0;"> <span id="LC975" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
982
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<pre style="margin: 0;">-<span id="LC982" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">merged_header_needed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fwd_header_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix_len</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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983
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<pre style="margin: 0;">-<span id="LC983" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
984
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<pre style="margin: 0;">-<span id="LC984" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merged_header_needed</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_header_alloc</span><span class="p">)</span></span>
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985
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<pre style="margin: 0;">-<span id="LC985" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
986
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<pre style="margin: 0;">-<span id="LC986" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_header_alloc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merged_header_needed</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
987
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<pre style="margin: 0;">-<span id="LC987" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_header</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;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_header</span><span class="p">,</span></span>
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988
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<pre style="margin: 0;">-<span id="LC988" class="line" lang="cpp"> <span class="n" style="color: #333;">merged_header_needed</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC989" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC990" class="line" lang="cpp"></span>
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976
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<pre style="margin: 0;"> <span id="LC976" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* make local copies of the seq, header and qual */</span></span>
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977
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<pre style="margin: 0;"> <span id="LC977" class="line" lang="cpp"></span>
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978
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<pre style="margin: 0;"> <span id="LC978" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fwd_header</span><span class="p">,</span> <span class="n" style="color: #333;">fastq_get_header</span><span class="p">(</span><span class="n" style="color: #333;">fastq_fwd</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="982" style="width: 35px; color: rgba(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">@@ -997,7 +982,6 @@ bool read_pair(merge_data_t * ip)</td>
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997
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982
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<pre style="margin: 0;"> <span id="LC982" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fwd_quality</span><span class="p">,</span> <span class="n" style="color: #333;">fastq_get_quality</span><span class="p">(</span><span class="n" style="color: #333;">fastq_fwd</span><span class="p">));</span></span>
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998
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983
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<pre style="margin: 0;"> <span id="LC983" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rev_quality</span><span class="p">,</span> <span class="n" style="color: #333;">fastq_get_quality</span><span class="p">(</span><span class="n" style="color: #333;">fastq_rev</span><span class="p">));</span></span>
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999
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984
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<pre style="margin: 0;"> <span id="LC984" class="line" lang="cpp"></span>
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1000
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<pre style="margin: 0;">-<span id="LC1000" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_header</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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1001
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985
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<pre style="margin: 0;"> <span id="LC985" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_sequence</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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1002
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986
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<pre style="margin: 0;"> <span id="LC986" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_quality</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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1003
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987
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<pre style="margin: 0;"> <span id="LC987" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</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="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="1035" style="width: 35px; color: rgba(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="1019" style="width: 35px; color: rgba(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">@@ -1035,8 +1019,6 @@ void init_merge_data(merge_data_t * ip)</td>
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1035
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1019
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<pre style="margin: 0;"> <span id="LC1019" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">reason</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">undefined</span><span class="p">;</span></span>
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1036
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1020
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<pre style="margin: 0;"> <span id="LC1020" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_seq_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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1037
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1021
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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_sequence</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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1038
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<pre style="margin: 0;">-<span id="LC1038" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_header</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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1039
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<pre style="margin: 0;">-<span id="LC1039" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_header_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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1040
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1022
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<pre style="margin: 0;"> <span id="LC1022" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_quality</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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1041
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1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="cpp"> <span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1024
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<pre style="margin: 0;"> <span id="LC1024" 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">@@ -1056,8 +1038,6 @@ void free_merge_data(merge_data_t * ip)</td>
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1056
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1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rev_quality</span><span class="p">)</span></span>
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1057
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1039
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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rev_quality</span><span class="p">);</span></span>
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1058
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1040
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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="cpp"></span>
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1059
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<pre style="margin: 0;">-<span id="LC1059" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_header</span><span class="p">)</span></span>
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1060
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<pre style="margin: 0;">-<span id="LC1060" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_header</span><span class="p">);</span></span>
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1061
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1041
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<pre style="margin: 0;"> <span id="LC1041" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_sequence</span><span class="p">)</span></span>
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1062
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1042
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<pre style="margin: 0;"> <span id="LC1042" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_sequence</span><span class="p">);</span></span>
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1063
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1043
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<pre style="margin: 0;"> <span id="LC1043" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merged_quality</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#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">@@ -323,6 +323,13 @@ void sintax_query(int64_t t)</td>
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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="LC333" 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="LC334" 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="LC335" 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">@@ -344,10 +351,6 @@ void sintax_query(int64_t t)</td>
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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="LC352" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* perform 100 bootstraps */</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">best_count</span><span class="p">[</span><span class="n" style="color: #333;">s</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="LC348" class="line" lang="cpp"> <span class="n" style="color: #333;">best_seqno</span><span class="p">[</span><span class="n" style="color: #333;">s</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="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">boot_count</span><span class="p">[</span><span class="n" style="color: #333;">s</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="LC350" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">kmersamplecount</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">subset_size</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;">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;">bootstrap_count</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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<li id="a9f0536a1f6138188dbd33cace26c5ff3c05cb39">
<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#a9f0536a1f6138188dbd33cace26c5ff3c05cb39"><strong>src/sortbylength.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">@@ -60,7 +60,7 @@</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"></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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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_s</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_<span class="idiff left right">length_</span>s</span></span>
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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="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;">length</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC66" 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;">size</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">@@ -69,8 +69,8 @@ static struct sortinfo_s</td>
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">sortbylength_compare</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><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;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_<span class="idiff left">s</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff right">sortinfo</span>_s</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">a</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;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_<span class="idiff left">s</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff right">sortinfo</span>_s</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">b</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;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_<span class="idiff left">length_s</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff right">sortinfo_length</span>_s</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">a</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;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_<span class="idiff left">length_s</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff right">sortinfo_length</span>_s</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* longest first, then most abundant, then by label, otherwise keep order */</span></span>
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<pre style="margin: 0;"> <span id="LC76" 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">@@ -110,7 +110,8 @@ void sortbylength()</td>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">show_rusage</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dbsequencecount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">db_getsequencecount</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">sortinfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_s</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">xmalloc</span><span class="p">(</span><span class="n" style="color: #333;">dbsequencecount</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">sortinfo_s</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">sortinfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_length_s</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">xmalloc</span><span class="p">(</span><span class="n" style="color: #333;">dbsequencecount</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">sortinfo_length_s</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">passed</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="LC117" 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">@@ -127,7 +128,7 @@ void sortbylength()</td>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">show_rusage</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_init</span><span class="p">(</span><span class="s" style="color: #d14;">"Sorting"</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><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;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">sortinfo</span><span class="p">,</span> <span class="n" style="color: #333;">passed</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">sortinfo_s</span><span class="p">),</span> <span class="n" style="color: #333;">sortbylength_compare</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="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">sortinfo</span><span class="p">,</span> <span class="n" style="color: #333;">passed</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">sortinfo_<span class="idiff left right">length_</span>s</span><span class="p">),</span> <span class="n" style="color: #333;">sortbylength_compare</span><span class="p">);</span></span>
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131
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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;">progress_done</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"></span>
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133
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">median</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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<li id="28d5028d98d0db6236ac6ceb7aa6d9237356403c">
<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#28d5028d98d0db6236ac6ceb7aa6d9237356403c"><strong>src/sortbysize.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">@@ -60,7 +60,7 @@</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"></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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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_s</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_s<span class="idiff left right">ize_s</span></span></span>
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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="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;">size</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC66" 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;">seqno</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">@@ -68,8 +68,8 @@ static struct sortinfo_s</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">sortbysize_compare</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><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;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_s</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">x</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff right">sortinfo</span>_s</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">a</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;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_s</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">y</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff right">sortinfo</span>_s</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">b</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;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_s<span class="idiff left">ize_s</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff right">sortinfo_size</span>_s</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">a</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;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_s<span class="idiff left">ize_s</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff right">sortinfo_size</span>_s</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* highest abundance first, then by label, otherwise keep order */</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -108,7 +108,8 @@ void sortbysize()</td>
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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="n" style="color: #333;">progress_init</span><span class="p">(</span><span class="s" style="color: #d14;">"Getting sizes"</span><span class="p">,</span> <span class="n" style="color: #333;">dbsequencecount</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">sortinfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_s</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">xmalloc</span><span class="p">(</span><span class="n" style="color: #333;">dbsequencecount</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">sortinfo_s</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">sortinfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">sortinfo_size_s</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">xmalloc</span><span class="p">(</span><span class="n" style="color: #333;">dbsequencecount</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">sortinfo_size_s</span><span class="p">));</span></span>
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">passed</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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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="131" style="width: 35px; color: rgba(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">@@ -130,7 +131,7 @@ void sortbysize()</td>
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130
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">show_rusage</span><span class="p">();</span></span>
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131
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"></span>
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132
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_init</span><span class="p">(</span><span class="s" style="color: #d14;">"Sorting"</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">sortinfo</span><span class="p">,</span> <span class="n" style="color: #333;">passed</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">sortinfo_s</span><span class="p">),</span> <span class="n" style="color: #333;">sortbysize_compare</span><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 class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">sortinfo</span><span class="p">,</span> <span class="n" style="color: #333;">passed</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">sortinfo_s<span class="idiff left right">ize_s</span></span><span class="p">),</span> <span class="n" style="color: #333;">sortbysize_compare</span><span class="p">);</span></span>
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134
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">progress_done</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>
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136
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">median</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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<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#b0109d980457466d1deec0f79c45e2b54114fdd5"><strong>src/vsearch.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,6 +102,7 @@ char * opt_db;</td>
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102
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102
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<pre style="margin: 0;"> <span id="LC102" 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_dbmatched</span><span class="p">;</span></span>
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103
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103
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<pre style="margin: 0;"> <span id="LC103" 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_dbnotmatched</span><span class="p">;</span></span>
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104
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104
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<pre style="margin: 0;"> <span id="LC104" 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_derep_fulllength</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" 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_derep_id</span><span class="p">;</span></span>
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105
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106
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<pre style="margin: 0;"> <span id="LC106" 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_derep_prefix</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;"> <span id="LC107" 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_eetabbedout</span><span class="p">;</span></span>
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107
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108
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<pre style="margin: 0;"> <span id="LC108" 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_fastaout</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="675" style="width: 35px; color: rgba(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">@@ -675,6 +676,7 @@ void args_init(int argc, char **argv)</td>
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675
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_dbmatched</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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676
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677
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_dbnotmatched</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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677
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678
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_derep_fulllength</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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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_derep_id</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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678
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680
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_derep_prefix</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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679
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681
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_dn</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.4</span><span class="p">;</span></span>
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680
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682
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_ee_cutoffs_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="782" style="width: 35px; color: rgba(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="784" style="width: 35px; color: rgba(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">@@ -782,7 +784,7 @@ void args_init(int argc, char **argv)</td>
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782
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784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_maxaccepts</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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783
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_maxdiffs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INT_MAX</span><span class="p">;</span></span>
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784
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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_maxgaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INT_MAX</span><span class="p">;</span></span>
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785
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<pre style="margin: 0;">-<span id="LC785" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_maxhits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">LONG_MAX</span></span><span class="p">;</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_maxhits</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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786
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_maxid</span> <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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787
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_maxqsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INT_MAX</span><span class="p">;</span></span>
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788
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790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_maxqt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DBL_MAX</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="914" style="width: 35px; color: rgba(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="916" style="width: 35px; color: rgba(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">@@ -914,6 +916,7 @@ void args_init(int argc, char **argv)</td>
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914
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916
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<pre style="margin: 0;"> <span id="LC916" class="line" lang="cpp"> <span class="n" style="color: #333;">option_dbmatched</span><span class="p">,</span></span>
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915
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917
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<pre style="margin: 0;"> <span id="LC917" class="line" lang="cpp"> <span class="n" style="color: #333;">option_dbnotmatched</span><span class="p">,</span></span>
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916
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918
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<pre style="margin: 0;"> <span id="LC918" class="line" lang="cpp"> <span class="n" style="color: #333;">option_derep_fulllength</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="cpp"> <span class="n" style="color: #333;">option_derep_id</span><span class="p">,</span></span>
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917
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920
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<pre style="margin: 0;"> <span id="LC920" class="line" lang="cpp"> <span class="n" style="color: #333;">option_derep_prefix</span><span class="p">,</span></span>
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918
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921
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<pre style="margin: 0;"> <span id="LC921" class="line" lang="cpp"> <span class="n" style="color: #333;">option_dn</span><span class="p">,</span></span>
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919
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922
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<pre style="margin: 0;"> <span id="LC922" class="line" lang="cpp"> <span class="n" style="color: #333;">option_ee_cutoffs</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1142" style="width: 35px; color: rgba(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="1145" style="width: 35px; color: rgba(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">@@ -1142,6 +1145,7 @@ void args_init(int argc, char **argv)</td>
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1142
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1145
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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"dbmatched"</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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1143
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1146
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<pre style="margin: 0;"> <span id="LC1146" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"dbnotmatched"</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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1144
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1147
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"derep_fulllength"</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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1148
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"derep_id"</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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1145
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1149
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<pre style="margin: 0;"> <span id="LC1149" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"derep_prefix"</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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1146
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1150
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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"dn"</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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1147
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1151
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<pre style="margin: 0;"> <span id="LC1151" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"ee_cutoffs"</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2287" style="width: 35px; color: rgba(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="2291" style="width: 35px; color: rgba(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">@@ -2287,6 +2291,10 @@ void args_init(int argc, char **argv)</td>
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2287
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2291
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<pre style="margin: 0;"> <span id="LC2291" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_relabel_self</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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2288
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2292
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<pre style="margin: 0;"> <span id="LC2292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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2289
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<td class="diff-line-num new_line" data-linenumber="2293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2293
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<pre style="margin: 0;"> <span id="LC2293" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="2294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2294
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<pre style="margin: 0;">+<span id="LC2294" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">option_derep_id</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2295
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<pre style="margin: 0;">+<span id="LC2295" 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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<pre style="margin: 0;">+<span id="LC2296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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2297
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<pre style="margin: 0;">+<span id="LC2297" class="line" lang="cpp"></span>
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2290
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2298
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<pre style="margin: 0;"> <span id="LC2298" class="line" lang="cpp"> <span class="nl">default:</span></span>
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2291
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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;">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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2292
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2300
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<pre style="margin: 0;"> <span id="LC2300" 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="2311" style="width: 35px; color: rgba(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="2319" style="width: 35px; color: rgba(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">@@ -2311,6 +2319,7 @@ void args_init(int argc, char **argv)</td>
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2311
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2319
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<pre style="margin: 0;"> <span id="LC2319" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cluster_unoise</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="2312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2312
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<td class="diff-line-num new_line" data-linenumber="2320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2320
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<pre style="margin: 0;"> <span id="LC2320" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cut</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="2313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2313
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2321
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<pre style="margin: 0;"> <span id="LC2321" class="line" lang="cpp"> <span class="n" style="color: #333;">option_derep_fulllength</span><span class="p">,</span></span>
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2322
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<pre style="margin: 0;">+<span id="LC2322" class="line" lang="cpp"> <span class="n" style="color: #333;">option_derep_id</span><span class="p">,</span></span>
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2314
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2323
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<pre style="margin: 0;"> <span id="LC2323" class="line" lang="cpp"> <span class="n" style="color: #333;">option_derep_prefix</span><span class="p">,</span></span>
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2315
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2324
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<pre style="margin: 0;"> <span id="LC2324" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_chars</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="2316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2316
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2325
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<pre style="margin: 0;"> <span id="LC2325" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_convert</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2858" style="width: 35px; color: rgba(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="2867" style="width: 35px; color: rgba(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">@@ -2858,6 +2867,34 @@ void args_init(int argc, char **argv)</td>
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2858
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2867
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<pre style="margin: 0;"> <span id="LC2867" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="2859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2859
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<td class="diff-line-num new_line" data-linenumber="2868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2868
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<pre style="margin: 0;"> <span id="LC2868" 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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<td class="diff-line-num old_line" data-linenumber="2860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2860
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2869
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<pre style="margin: 0;"> <span id="LC2869" class="line" lang="cpp"></span>
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2870
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<pre style="margin: 0;">+<span id="LC2870" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">option_derep_id</span><span class="p">,</span></span>
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2871
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<pre style="margin: 0;">+<span id="LC2871" class="line" lang="cpp"> <span class="n" style="color: #333;">option_bzip2_decompress</span><span class="p">,</span></span>
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2872
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<pre style="margin: 0;">+<span id="LC2872" 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 new new_line" data-linenumber="2873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2873
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<pre style="margin: 0;">+<span id="LC2873" 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="diff-line-num new new_line" data-linenumber="2874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2874
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<pre style="margin: 0;">+<span id="LC2874" class="line" lang="cpp"> <span class="n" style="color: #333;">option_log</span><span class="p">,</span></span>
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2875
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<pre style="margin: 0;">+<span id="LC2875" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxseqlength</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2876
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<pre style="margin: 0;">+<span id="LC2876" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxuniquesize</span><span class="p">,</span></span>
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2877
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<pre style="margin: 0;">+<span id="LC2877" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minseqlength</span><span class="p">,</span></span>
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2878
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<pre style="margin: 0;">+<span id="LC2878" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minuniquesize</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2879
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<pre style="margin: 0;">+<span id="LC2879" class="line" lang="cpp"> <span class="n" style="color: #333;">option_no_progress</span><span class="p">,</span></span>
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2880
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<pre style="margin: 0;">+<span id="LC2880" class="line" lang="cpp"> <span class="n" style="color: #333;">option_notrunclabels</span><span class="p">,</span></span>
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2881
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<pre style="margin: 0;">+<span id="LC2881" class="line" lang="cpp"> <span class="n" style="color: #333;">option_output</span><span class="p">,</span></span>
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2882
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<pre style="margin: 0;">+<span id="LC2882" class="line" lang="cpp"> <span class="n" style="color: #333;">option_quiet</span><span class="p">,</span></span>
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2883
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<pre style="margin: 0;">+<span id="LC2883" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2884
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<pre style="margin: 0;">+<span id="LC2884" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2885
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<pre style="margin: 0;">+<span id="LC2885" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2886
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<pre style="margin: 0;">+<span id="LC2886" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2887
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<pre style="margin: 0;">+<span id="LC2887" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2888
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<pre style="margin: 0;">+<span id="LC2888" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2889
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<pre style="margin: 0;">+<span id="LC2889" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
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2890
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<pre style="margin: 0;">+<span id="LC2890" class="line" lang="cpp"> <span class="n" style="color: #333;">option_strand</span><span class="p">,</span></span>
</pre>
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2891
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<pre style="margin: 0;">+<span id="LC2891" class="line" lang="cpp"> <span class="n" style="color: #333;">option_threads</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2892
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<pre style="margin: 0;">+<span id="LC2892" class="line" lang="cpp"> <span class="n" style="color: #333;">option_topn</span><span class="p">,</span></span>
</pre>
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2893
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<pre style="margin: 0;">+<span id="LC2893" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uc</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2894
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<pre style="margin: 0;">+<span id="LC2894" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xee</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2895
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<pre style="margin: 0;">+<span id="LC2895" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span><span class="p">,</span></span>
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2896
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<pre style="margin: 0;">+<span id="LC2896" 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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2897
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<pre style="margin: 0;">+<span id="LC2897" class="line" lang="cpp"></span>
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2861
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2898
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<pre style="margin: 0;"> <span id="LC2898" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">option_derep_prefix</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="2862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2862
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<td class="diff-line-num new_line" data-linenumber="2899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2899
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<pre style="margin: 0;"> <span id="LC2899" 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="diff-line-num old_line" data-linenumber="2863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2863
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<td class="diff-line-num new_line" data-linenumber="2900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2900
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<pre style="margin: 0;"> <span id="LC2900" 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="3046" style="width: 35px; color: rgba(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="3083" style="width: 35px; color: rgba(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">@@ -3046,6 +3083,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3046
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<td class="diff-line-num new_line" data-linenumber="3083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3083
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<pre style="margin: 0;"> <span id="LC3083" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_qmax</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3047
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<td class="diff-line-num new_line" data-linenumber="3084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3084
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<pre style="margin: 0;"> <span id="LC3084" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_qmaxout</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3048
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<td class="diff-line-num new_line" data-linenumber="3085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3085
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<pre style="margin: 0;"> <span id="LC3085" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_qmin</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3086
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<pre style="margin: 0;">+<span id="LC3086" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_qminout</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3049
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<td class="diff-line-num new_line" data-linenumber="3087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3087
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<pre style="margin: 0;"> <span id="LC3087" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_truncqual</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3050
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3088
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<pre style="margin: 0;"> <span id="LC3088" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastqout</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3051
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3089
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<pre style="margin: 0;"> <span id="LC3089" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastqout_notmerged_fwd</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4056" style="width: 35px; color: rgba(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="4094" style="width: 35px; color: rgba(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">@@ -4056,6 +4094,9 @@ void args_init(int argc, char **argv)</td>
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4056
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4094
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<pre style="margin: 0;"> <span id="LC4094" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_maxsize</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4057
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<td class="diff-line-num new_line" data-linenumber="4095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4095
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<pre style="margin: 0;"> <span id="LC4095" 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 maxsize must be at least 1"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4058
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<td class="diff-line-num new_line" data-linenumber="4096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4096
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<pre style="margin: 0;"> <span id="LC4096" class="line" lang="cpp"></span>
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<td class="diff-line-num new old_line" data-linenumber="4059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4097
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<pre style="margin: 0;">+<span id="LC4097" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_maxhits</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4098
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<pre style="margin: 0;">+<span id="LC4098" 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 maxhits cannot be negative"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4099
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<pre style="margin: 0;">+<span id="LC4099" class="line" lang="cpp"></span>
</pre>
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4059
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4100
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<pre style="margin: 0;"> <span id="LC4100" class="line" lang="cpp"></span>
</pre>
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4060
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<td class="diff-line-num new_line" data-linenumber="4101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4101
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<pre style="margin: 0;"> <span id="LC4101" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* TODO: check valid range of gap penalties */</span></span>
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4061
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4102
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<pre style="margin: 0;"> <span id="LC4102" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4086" style="width: 35px; color: rgba(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="4127" style="width: 35px; color: rgba(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">@@ -4086,6 +4127,9 @@ void args_init(int argc, char **argv)</td>
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4086
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4127
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<pre style="margin: 0;"> <span id="LC4127" class="line" lang="cpp"></span>
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4087
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<td class="diff-line-num new_line" data-linenumber="4128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4128
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<pre style="margin: 0;"> <span id="LC4128" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* set defaults parameters, if not specified */</span></span>
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4088
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4129
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<pre style="margin: 0;"> <span id="LC4129" class="line" lang="cpp"></span>
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4130
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<pre style="margin: 0;">+<span id="LC4130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_maxhits</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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4131
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<pre style="margin: 0;">+<span id="LC4131" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_maxhits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LONG_MAX</span><span class="p">;</span></span>
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4132
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<pre style="margin: 0;">+<span id="LC4132" class="line" lang="cpp"></span>
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4089
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4133
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<pre style="margin: 0;"> <span id="LC4133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_minwordmatches</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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4090
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<td class="diff-line-num new_line" data-linenumber="4134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4134
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<pre style="margin: 0;"> <span id="LC4134" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_minwordmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minwordmatches_defaults</span><span class="p">[</span><span class="n" style="color: #333;">opt_wordlength</span><span class="p">];</span></span>
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4091
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4135
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<pre style="margin: 0;"> <span id="LC4135" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4111" style="width: 35px; color: rgba(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="4155" style="width: 35px; color: rgba(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">@@ -4111,13 +4155,23 @@ void args_init(int argc, char **argv)</td>
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4111
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4155
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<pre style="margin: 0;"> <span id="LC4155" class="line" lang="cpp"></span>
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4112
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4156
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<pre style="margin: 0;"> <span id="LC4156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_minseqlength</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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4113
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4157
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<pre style="margin: 0;"> <span id="LC4157" class="line" lang="cpp"> <span class="p">{</span></span>
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4114
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<pre style="margin: 0;">-<span id="LC4114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_cluster_smallmem</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_cluster_fast</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_cluster_size</span> <span class="o" style="font-weight: 600;">||</span></span>
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4115
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<pre style="margin: 0;">-<span id="LC4115" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_usearch_global</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_derep_fulllength</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_derep_prefix</span> <span class="o" style="font-weight: 600;">||</span></span>
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4116
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<pre style="margin: 0;">-<span id="LC4116" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_makeudb_usearch</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_cluster_unoise</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_sintax</span><span class="p">)</span></span>
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4158
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<pre style="margin: 0;">+<span id="LC4158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_cluster_fast</span> <span class="o" style="font-weight: 600;">||</span></span>
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4159
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<pre style="margin: 0;">+<span id="LC4159" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_cluster_size</span> <span class="o" style="font-weight: 600;">||</span></span>
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4160
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<pre style="margin: 0;">+<span id="LC4160" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_cluster_smallmem</span> <span class="o" style="font-weight: 600;">||</span></span>
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4161
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<pre style="margin: 0;">+<span id="LC4161" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_cluster_unoise</span> <span class="o" style="font-weight: 600;">||</span></span>
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4162
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<pre style="margin: 0;">+<span id="LC4162" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_derep_fulllength</span> <span class="o" style="font-weight: 600;">||</span></span>
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4163
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<pre style="margin: 0;">+<span id="LC4163" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_derep_id</span> <span class="o" style="font-weight: 600;">||</span></span>
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4164
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<pre style="margin: 0;">+<span id="LC4164" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_derep_prefix</span> <span class="o" style="font-weight: 600;">||</span></span>
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4165
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<pre style="margin: 0;">+<span id="LC4165" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_makeudb_usearch</span> <span class="o" style="font-weight: 600;">||</span></span>
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4166
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<pre style="margin: 0;">+<span id="LC4166" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_sintax</span> <span class="o" style="font-weight: 600;">||</span></span>
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4167
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<pre style="margin: 0;">+<span id="LC4167" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_usearch_global</span><span class="p">)</span></span>
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4117
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4168
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<pre style="margin: 0;"> <span id="LC4168" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_minseqlength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>
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4118
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4169
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<pre style="margin: 0;"> <span id="LC4169" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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4119
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4170
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<pre style="margin: 0;"> <span id="LC4170" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_minseqlength</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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4120
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4171
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<pre style="margin: 0;"> <span id="LC4171" class="line" lang="cpp"> <span class="p">}</span></span>
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4172
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<pre style="margin: 0;">+<span id="LC4172" class="line" lang="cpp"></span>
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4173
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<pre style="margin: 0;">+<span id="LC4173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_sintax</span><span class="p">)</span></span>
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4174
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<pre style="margin: 0;">+<span id="LC4174" 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;">1</span><span class="p">;</span></span>
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4121
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4175
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<pre style="margin: 0;"> <span id="LC4175" class="line" lang="cpp"><span class="p">}</span></span>
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4122
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4176
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<pre style="margin: 0;"> <span id="LC4176" class="line" lang="cpp"></span>
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4123
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4177
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<pre style="margin: 0;"> <span id="LC4177" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">show_publication</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4267" style="width: 35px; color: rgba(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="4321" style="width: 35px; color: rgba(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">@@ -4267,6 +4321,7 @@ void cmd_help()</td>
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4267
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4321
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<pre style="margin: 0;"> <span id="LC4321" 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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4268
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4322
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<pre style="margin: 0;"> <span id="LC4322" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Dereplication and rereplication</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 old_line" data-linenumber="4269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4269
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<td class="diff-line-num new_line" data-linenumber="4323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4323
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<pre style="margin: 0;"> <span id="LC4323" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --derep_fulllength FILENAME dereplicate sequences in the given FASTA file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4324
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<pre style="margin: 0;">+<span id="LC4324" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --derep_id FILENAME dereplicate using both identifiers and sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4270
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<td class="diff-line-num new_line" data-linenumber="4325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4325
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<pre style="margin: 0;"> <span id="LC4325" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --derep_prefix FILENAME dereplicate sequences in file based on prefixes</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 old_line" data-linenumber="4271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4271
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<td class="diff-line-num new_line" data-linenumber="4326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4326
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<pre style="margin: 0;"> <span id="LC4326" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --rereplicate FILENAME rereplicate sequences in the given FASTA file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4272
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<td class="diff-line-num new_line" data-linenumber="4327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4327
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<pre style="margin: 0;"> <span id="LC4327" class="line" lang="cpp"> <span class="s" style="color: #d14;">" Parameters</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="4379" style="width: 35px; color: rgba(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="4434" style="width: 35px; color: rgba(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">@@ -4379,7 +4434,7 @@ void cmd_help()</td>
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4379
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4434
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<pre style="margin: 0;"> <span id="LC4434" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastqout FILENAME FASTQ output filename for merged sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4380
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4435
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<pre style="margin: 0;"> <span id="LC4435" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastqout_notmerged_fwd FN FASTQ filename for non-merged forward sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4381
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4436
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<pre style="margin: 0;"> <span id="LC4436" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastqout_notmerged_rev FN FASTQ filename for non-merged reverse sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4382
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<pre style="margin: 0;">-<span id="LC4382" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --label_suffix <span class="idiff left right"> </span> suffix to append to label of merged sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4437
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<pre style="margin: 0;">+<span id="LC4437" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --label_suffix <span class="idiff left right">STRING</span> suffix to append to label of merged sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4383
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4438
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<pre style="margin: 0;"> <span id="LC4438" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --xee remove expected errors (ee) info from output</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4384
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4439
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<pre style="margin: 0;"> <span id="LC4439" 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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4385
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4440
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<pre style="margin: 0;"> <span id="LC4440" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Pairwise alignment</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="4673" style="width: 35px; color: rgba(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="4728" style="width: 35px; color: rgba(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">@@ -4673,6 +4728,8 @@ void cmd_derep()</td>
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4673
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4728
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<pre style="margin: 0;"> <span id="LC4728" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="4674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4674
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4729
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<pre style="margin: 0;"> <span id="LC4729" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_derep_fulllength</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="4675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4675
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4730
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<pre style="margin: 0;"> <span id="LC4730" class="line" lang="cpp"> <span class="n" style="color: #333;">derep_fulllength</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4731
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<pre style="margin: 0;">+<span id="LC4731" 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_derep_id</span><span class="p">)</span></span>
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4732
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<pre style="margin: 0;">+<span id="LC4732" class="line" lang="cpp"> <span class="n" style="color: #333;">derep_id</span><span class="p">();</span></span>
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4676
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<td class="diff-line-num new_line" data-linenumber="4733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4733
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<pre style="margin: 0;"> <span id="LC4733" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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4677
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4734
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<pre style="margin: 0;"> <span id="LC4734" class="line" lang="cpp"> <span class="p">{</span></span>
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4678
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4735
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<pre style="margin: 0;"> <span id="LC4735" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4965" style="width: 35px; color: rgba(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="5022" style="width: 35px; color: rgba(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">@@ -4965,7 +5022,7 @@ int main(int argc, char** argv)</td>
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4965
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5022
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<pre style="margin: 0;"> <span id="LC5022" class="line" lang="cpp"> <span class="n" style="color: #333;">cmd_sortbysize</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="4966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4966
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<td class="diff-line-num new_line" data-linenumber="5023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5023
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<pre style="margin: 0;"> <span id="LC5023" 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_sortbylength</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="4967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4967
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<td class="diff-line-num new_line" data-linenumber="5024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5024
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<pre style="margin: 0;"> <span id="LC5024" class="line" lang="cpp"> <span class="n" style="color: #333;">cmd_sortbylength</span><span class="p">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4968
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<td class="diff-line-num new_line old" data-linenumber="5025" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC4968" 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_derep_fulllength</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_derep_prefix</span><span class="p">)</span></span>
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5025
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<pre style="margin: 0;">+<span id="LC5025" 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_derep_fulllength</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_derep_<span class="idiff left">id</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">opt_derep_</span>prefix</span><span class="p">)</span></span>
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4969
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5026
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<pre style="margin: 0;"> <span id="LC5026" class="line" lang="cpp"> <span class="n" style="color: #333;">cmd_derep</span><span class="p">();</span></span>
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4970
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5027
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<pre style="margin: 0;"> <span id="LC5027" 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_shuffle</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="4971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4971
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5028
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<pre style="margin: 0;"> <span id="LC5028" class="line" lang="cpp"> <span class="n" style="color: #333;">cmd_shuffle</span><span class="p">();</span></span>
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<li id="d5c50f833cab4828d6d2b3f54dda35a42237db09">
<a href="https://salsa.debian.org/med-team/vsearch/-/compare/647be73e11398303a4ca69bc41a4ba2669634548...91780227165a2cd116ba9198a8bf8990fca730d9#d5c50f833cab4828d6d2b3f54dda35a42237db09"><strong>src/vsearch.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -291,6 +291,7 @@ extern char * opt_db;</td>
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291
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291
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<pre style="margin: 0;"> <span id="LC291" 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_dbmatched</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="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_dbnotmatched</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="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_derep_fulllength</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC294" 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_derep_id</span><span class="p">;</span></span>
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294
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<pre style="margin: 0;"> <span id="LC295" 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_derep_prefix</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC296" 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_eetabbedout</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC297" 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_fastaout</span><span class="p">;</span></span>
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