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<h3>
Steffen Möller pushed to branch upstream
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/a6e84605ff4ae3d2eb2fe51571bda5469e368a1e">a6e84605</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-29T13:31:44Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.14.1</pre>
</li>
</ul>
<h4>15 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
</a>
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<li class="file-stats">
<a href="#e9eacc068eb0149cb6567e67eb35ca6a728c05af">
man/Makefile.am
</a>
</li>
<li class="file-stats">
<a href="#b7ca4efea9812be2ea989e558de10e419bd9cf39">
man/vsearch.1
</a>
</li>
<li class="file-stats">
<a href="#d79e6705e3db119ee1bb6ad9670fe99b162c13b0">
src/cluster.cc
</a>
</li>
<li class="file-stats">
<a href="#67ef99e491c4bda5d0c47f152cae53d18d7fbcd3">
src/fasta.cc
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<li class="file-stats">
<a href="#dce607e2c5a20b2277b76421039058016c3f2150">
src/fasta.h
</a>
</li>
<li class="file-stats">
<a href="#d6ab431461af8e07f1ea378788017353266e8ba2">
src/fastq.cc
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<li class="file-stats">
<a href="#5158e97b06e3c2eb531bf6a179b392990120db5a">
src/filter.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="#bf4e2f7794da01f756a938b41abe5f10f972e887">
src/msa.cc
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<li class="file-stats">
<a href="#d6b1377ec11c4f9379910db0cc295c16f7dbf5e2">
src/sffconvert.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
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/vsearch/commit/a6e84605ff4ae3d2eb2fe51571bda5469e368a1e#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +10,7 @@ compiler:</td>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">clang</span></span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get install ghostscript; else brew install ghostscript; fi</span></span>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get install ghostscript; <span class="idiff left right">sudo apt-get install groff; </span>else brew install ghostscript; fi</span></span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">./autogen.sh</span></span>
</pre>
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<br>
</li>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/vsearch/commit/a6e84605ff4ae3d2eb2fe51571bda5469e368a1e#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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<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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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"></span>
</pre>
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<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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<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">3.6</span>/vsearch_manual.pdf</span><span class="p">)</span>, please visit the <span class="p">[</span><span class="nv" style="color: #008080;">VSEARCH Web Forum</span><span class="p">](</span><span class="sx" style="color: #d14;">https://groups.google.com/forum/#!forum/vsearch-forum</span><span class="p">)</span> to post a question or start a discussion.</span>
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<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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<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">4.1</span>/vsearch_manual.pdf</span><span class="p">)</span>, please visit the <span class="p">[</span><span class="nv" style="color: #008080;">VSEARCH Web Forum</span><span class="p">](</span><span class="sx" style="color: #d14;">https://groups.google.com/forum/#!forum/vsearch-forum</span><span class="p">)</span> to post a question or start a discussion.</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"></span>
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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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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"></span>
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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">3.6</span>.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown">tar xzf v2.1<span class="idiff left right">3.6</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">3.6</span></span>
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50
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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">4.1</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">4.1</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">4.1</span></span>
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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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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown">./configure</span>
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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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<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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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown"></span>
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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>
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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">3.6/vsearch-2.13.6</span>-linux-x86_64.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.1<span class="idiff left right">3.6</span>-linux-x86_64.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left right">4.1/vsearch-2.14.1</span>-linux-x86_64.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.1<span class="idiff left right">4.1</span>-linux-x86_64.tar.gz</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"></span>
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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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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"></span>
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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>
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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">3.6/vsearch-2.13.6</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">3.6</span>-linux-ppc64le.tar.gz</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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">4.1/vsearch-2.14.1</span>-linux-ppc64le.tar.gz</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.1<span class="idiff left right">4.1</span>-linux-ppc64le.tar.gz</span>
</pre>
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90
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<td class="diff-line-num new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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<td class="diff-line-num old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
91
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
92
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<td class="diff-line-num new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
94
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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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">3.6/vsearch-2.13.6</span>-linux-aarch64.tar.gz</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
96
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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="LC96" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.1<span class="idiff left right">3.6</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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<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">4.1/vsearch-2.14.1</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">4.1</span>-linux-aarch64.tar.gz</span>
</pre>
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<td class="diff-line-num old_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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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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<td class="diff-line-num new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
100
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span 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">3.6/vsearch-2.13.6</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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<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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<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">3.6</span>-macos-x86_64.tar.gz</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="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="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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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="LC102" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left right">4.1/vsearch-2.14.1</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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<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">4.1</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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC104" class="line" lang="markdown"><span class="p">```</span></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="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
</td>
<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>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
107
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<td class="diff-line-num new_line" data-linenumber="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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<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="markdown">https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left right">3.6/vsearch-2.13.6</span>-win-x86_64.zip</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown">https://github.com/torognes/vsearch/releases/download/v2.1<span class="idiff left right">4.1/vsearch-2.14.1</span>-win-x86_64.zip</span>
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110
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"><span class="p">```</span></span>
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111
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"></span>
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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">3.6-linux-x86_64`</span></span><span class="idiff"> or </span><span class="sb" style="color: #d14;"><span class="idiff right">`vsearch-2.13.6</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;">`$MANPATH`</span>. The PDF version of the manual is available in <span class="sb" style="color: #d14;">`doc/vsearch_manual.pdf`</span>.</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown">Linux and Mac: You will now have the binary distribution in a folder called <span class="sb" style="color: #d14;">`vsearch-2.1<span class="idiff left">4.1-linux-x86_64`</span></span><span class="idiff"> or </span><span class="sb" style="color: #d14;"><span class="idiff right">`vsearch-2.14.1</span>-macos-x86_64`</span> in which you will find three subfolders <span class="sb" style="color: #d14;">`bin`</span>, <span class="sb" style="color: #d14;">`man`</span> and <span class="sb" style="color: #d14;">`doc`</span>. We recommend making a copy or a symbolic link to the vsearch binary <span class="sb" style="color: #d14;">`bin/vsearch`</span> in a folder included in your <span class="sb" style="color: #d14;">`$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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114
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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">3.6</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">4.1</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>
</pre>
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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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<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
117
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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">3.6/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/v2.13.6</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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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="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">4.1/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/v2.14.1</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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118
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"></span>
</pre>
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119
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown"></span>
</pre>
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120
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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/commit/a6e84605ff4ae3d2eb2fe51571bda5469e368a1e#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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2
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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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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AC_PREREQ([2.63])</span>
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5
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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">3.6</span>], [torognes@ifi.uio.no])</span>
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5
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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">4.1</span>], [torognes@ifi.uio.no])</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">AC_CANONICAL_TARGET</span>
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7
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">AM_INIT_AUTOMAKE([subdir-objects])</span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">AC_LANG([C++])</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" style="width: 35px; color: rgba(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="73" style="width: 35px; color: rgba(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">@@ -73,6 +73,8 @@ AS_IF([test "x$enable_pdfman" != "xno"], [</td>
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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"> fi</span>
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74
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext">])</span>
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75
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">have_man_html=no</span>
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<td class="diff-line-num new old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); 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="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
76
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">if test "x${have_pthreads}" = "xyes"; then</span>
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77
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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> AC_CHECK_HEADERS([pthread.h], [], [have_pthreads=no])</span>
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78
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">fi</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -96,6 +98,7 @@ AM_CONDITIONAL(HAVE_BZLIB, test "x${have_bzip2}" = "xyes")</td>
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<td class="diff-line-num old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
96
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext">AM_CONDITIONAL(HAVE_ZLIB, test "x${have_zlib}" = "xyes")</span>
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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
97
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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">AM_CONDITIONAL(HAVE_PTHREADS, test "x${have_pthreads}" = "xyes")</span>
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98
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<td class="diff-line-num new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">AM_CONDITIONAL(HAVE_PS2PDF, test "x${have_ps2pdf}" = "xyes")</span>
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<td class="diff-line-num new old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">AM_CONDITIONAL(HAVE_MAN_HTML, test "x${have_man_html}" = "xyes")</span>
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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="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext">AM_CONDITIONAL(TARGET_PPC, test "x${target_ppc}" = "xyes")</span>
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<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
100
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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">AM_CONDITIONAL(TARGET_AARCH64, test "x${target_aarch64}" = "xyes")</span>
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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="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="plaintext">AM_PROG_CC_C_O</span>
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</li>
<li id="e9eacc068eb0149cb6567e67eb35ca6a728c05af">
<a href="https://salsa.debian.org/med-team/vsearch/commit/a6e84605ff4ae3d2eb2fe51571bda5469e368a1e#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">@@ -2,21 +2,40 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"><span class="nv" style="color: #008080;">dist_man_MANS</span> <span class="o" style="font-weight: 600;">=</span> vsearch.1</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">doc_DATA</span> <span class="o" style="font-weight: 600;">=</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">CLEANFILES</span> <span class="o" style="font-weight: 600;">=</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">if</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">HAVE_MAN_HTML</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">doc_DATA</span> <span class="o" style="font-weight: 600;">+=</span> vsearch_manual.html</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="make"><span class="nl">vsearch_manual.html </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">vsearch.1</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\\-/-/g'</span> <span class="nv" style="color: #008080;">$<</span> | <span class="se" style="color: #d14;">\</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">$(uname)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"Darwin"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"> iconv <span class="nt" style="color: #000080;">-f</span> UTF-8 <span class="nt" style="color: #000080;">-t</span> ISO-8859-1 <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"> <span class="k" style="font-weight: 600;">else</span> <span class="se" style="color: #d14;">\</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cat</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span> | <span class="se" style="color: #d14;">\</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="make"> groff <span class="nt" style="color: #000080;">-t</span> <span class="nt" style="color: #000080;">-m</span> mandoc <span class="nt" style="color: #000080;">-m</span> www <span class="nt" style="color: #000080;">-Thtml</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$@</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"><span class="nv" style="color: #008080;">CLEANFILES</span> <span class="o" style="font-weight: 600;">+=</span> vsearch_manual.html</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"></span>
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25
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">if</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">HAVE_PS2PDF</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">doc_DATA</span> <span class="o" style="font-weight: 600;">=</span> vsearch_manual.pdf</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="make"><span class="nv" style="color: #008080;">doc_DATA</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">+</span>=</span> vsearch_manual.pdf</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"><span class="nl">vsearch_manual.pdf </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">vsearch.1</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">TEMP</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$$</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">mktemp </span></span><span class="idiff">temp.XXXXXXXX</span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">;</span></span> <span class="se" style="color: #d14;">\</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">sed</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-e</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'s/\\-/-/g'</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="idiff right"> |</span> <span class="se" style="color: #d14;">\</span></span>
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11
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">$(uname)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"Darwin"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\\-/-/g'</span> <span class="nv" style="color: #008080;">$<</span> | <span class="se" style="color: #d14;">\</span></span>
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13
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<td class="diff-line-num new_line old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="make"> iconv <span class="nt" style="color: #000080;">-f</span> UTF-8 <span class="nt" style="color: #000080;">-t</span> ISO-8859-1 <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$$</span>TEMP <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="make"> iconv <span class="nt" style="color: #000080;">-f</span> UTF-8 <span class="nt" style="color: #000080;">-t</span> ISO-8859-1 <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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14
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34
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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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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\\-/-/g'</span> <span class="nv" style="color: #008080;">$<</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$$</span>TEMP <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="make"> man <span class="nt" style="color: #000080;">-t</span> ./<span class="nv" style="color: #008080;">$$</span>TEMP | ps2pdf <span class="nt" style="color: #000080;">-sPAPERSIZE</span><span class="o" style="font-weight: 600;">=</span>a4 - <span class="nv" style="color: #008080;">$@</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nv" style="color: #008080;">$$</span>TEMP</span>
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35
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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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37
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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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19
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38
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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="LC20" class="line" lang="make"><span class="nv" style="color: #008080;">CLEANFILES</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span>vsearch_manual.pdf</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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff right"> </span>vsearch_manual.pdf</span>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make"></span>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/vsearch/commit/a6e84605ff4ae3d2eb2fe51571bda5469e368a1e#b7ca4efea9812be2ea989e558de10e419bd9cf39"><strong>man/vsearch.1</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" ============================================================================</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH vsearch 1 "<span class="idiff left right">July 2, 2019" "version 2.13.6</span>" "USER COMMANDS"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH vsearch 1 "<span class="idiff left right">September 18, 2019" "version 2.14.1</span>" "USER COMMANDS"</span>
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3
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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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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">vsearch \(em chimera detection, clustering, dereplication and</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -288,37 +288,48 @@ ambiguous (e.g. \-\-derep_f).</td>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="plaintext">.RE</span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">.TAG help-and-version-commands</span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="plaintext">Help and version commands:</span>
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="plaintext">.RS</span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="plaintext">.B \-\-help | \-\-h</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">.TAG help</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">.TAG h</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">.TP 9</span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">.B \-\-help \-\-h</span>
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295
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="plaintext">Display help text with brief information about all commands and</span>
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296
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="plaintext">options.</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">.TAG version</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">.TAG v</span>
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297
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="plaintext">.TP</span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="plaintext">.B \-\-version <span class="idiff left right">| </span>\-\-v</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">.B \-\-version \-\-v</span>
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299
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="plaintext">Output version information and a citation for the VSEARCH</span>
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300
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="plaintext">publication. Show the status of the support for gzip- and</span>
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301
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="plaintext">bzip2-compressed input files.</span>
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302
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="plaintext">.RE</span>
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303
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="plaintext">.PP</span>
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304
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">.TAG general-options</span>
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305
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="plaintext">General options:</span>
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306
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="plaintext">.RS</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">.TAG bzip2_decompress</span>
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307
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="plaintext">.TP 9</span>
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308
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="plaintext">.B \-\-bzip2_decompress</span>
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309
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="plaintext">When reading from a pipe streaming bzip2-compressed data, decompress</span>
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310
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="plaintext">the data. That option is not needed when reading from a standard</span>
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311
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<td class="diff-line-num new_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">
319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="plaintext">bzip2-compressed file.</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext">.TAG fasta_width</span>
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<td class="diff-line-num old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
312
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="plaintext">.TP</span>
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313
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="plaintext">.BI \-\-fasta_width\~ "positive integer"</span>
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314
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="plaintext">Fasta files produced by \fBvsearch\fR are wrapped (sequences are</span>
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315
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="plaintext">written on lines of \fIinteger\fR nucleotides, 80 by default). Set</span>
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316
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="plaintext">that value to zero to eliminate the wrapping.</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext">.TAG gzip_decompress</span>
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317
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="plaintext">.TP</span>
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318
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="plaintext">.B \-\-gzip_decompress</span>
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319
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="plaintext">When reading from a pipe streaming gzip-compressed data, decompress</span>
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320
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="plaintext">the data. That option is not needed when reading from a standard</span>
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321
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="plaintext">gzip-compressed file.</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext">.TAG log</span>
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="plaintext">.TP</span>
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323
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="plaintext">.BI \-\-log \0filename</span>
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324
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335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="plaintext">Write messages to the specified log file. Information written includes</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -328,26 +339,32 @@ and fatal errors. The start and finish times are also recorded as well</td>
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328
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="plaintext">as the elapsed time and the maximum amount of memory consumed. The</span>
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329
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="plaintext">different \fBvsearch\fR commands can also write additional</span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="plaintext">informations to the log file.</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext">.TAG maxseqlength</span>
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331
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="plaintext">.BI \-\-maxseqlength\~ "positive integer"</span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="plaintext">All \fBvsearch\fR operations discard sequences of length equal or</span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="plaintext">greater than \fIinteger\fR (50,000 nucleotides by default).</span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext">.TAG minseqlength</span>
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335
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="plaintext">.BI \-\-minseqlength\~ "positive integer"</span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="plaintext">All \fBvsearch\fR operations discard sequences of length smaller than</span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="plaintext">\fIinteger\fR: 1 nucleotide by default for sorting or shuffling, 32</span>
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339
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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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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext">.TAG no_progress</span>
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340
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="plaintext">.TP</span>
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341
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="plaintext">.B \-\-no_progress</span>
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="plaintext">Do not show the gradually increasing progress indicator.</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext">.TAG notrunclabels</span>
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343
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="plaintext">.TP</span>
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344
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="plaintext">.B \-\-notrunclabels</span>
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345
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360
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="plaintext">Do not truncate sequence labels at first space or tab, use the full</span>
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346
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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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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext">.TAG quiet</span>
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347
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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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348
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="plaintext">.B \-\-quiet</span>
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349
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="plaintext">Suppress all messages to stdout and stderr except for warnings and</span>
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350
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="plaintext">fatal error messages.</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext">.TAG threads</span>
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351
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="plaintext">.TP</span>
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352
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="plaintext">.BI \-\-threads\~ "positive integer"</span>
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353
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="plaintext">Number of computation threads to use (1 to 1024). The number of threads</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="378" style="width: 35px; color: rgba(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">@@ -361,6 +378,7 @@ the other commands.</td>
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361
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="plaintext">.RE</span>
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362
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="plaintext">.PP</span>
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363
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext">.TAG chimera-detection-options</span>
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364
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="plaintext">Chimera detection options:</span>
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365
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="plaintext">.PP</span>
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366
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="plaintext">.RS</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="399" style="width: 35px; color: rgba(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">@@ -381,6 +399,7 @@ sort sequences by decreasing abundance (default of</td>
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381
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="plaintext">\-\-derep_fulllength command). If your sequence set needs to be</span>
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382
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="plaintext">sorted, please see the \-\-sortbysize command in the sorting section.</span>
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383
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext">.TAG abskew</span>
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384
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="plaintext">.TP 9</span>
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385
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="plaintext">.BI \-\-abskew \0real</span>
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386
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="plaintext">When using \-\-uchime_denovo, the abundance skew is used to</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">@@ -391,20 +410,24 @@ their parents. For \-\-uchime3_denovo the default value is 16.0. For</td>
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391
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="plaintext">the other commands, the default value is 2.0, which means that the</span>
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392
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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="plaintext">parents should be at least 2 times more abundant than their</span>
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393
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="plaintext">chimera. Any positive value equal or greater than 1.0 can be used.</span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="plaintext">.TAG alignwidth</span>
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394
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="plaintext">.TP</span>
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395
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415
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="plaintext">.BI \-\-alignwidth\~ "positive integer"</span>
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396
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416
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="plaintext">When using \-\-uchimealns, set the width of the three-way alignments</span>
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397
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="plaintext">(80 nucleotides by default). Set to zero to eliminate wrapping.</span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext">.TAG borderline</span>
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398
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="plaintext">.TP</span>
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399
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="plaintext">.BI \-\-borderline \0filename</span>
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400
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421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="plaintext">Output borderline chimeric sequences to \fIfilename\fR, in fasta</span>
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401
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="plaintext">format. Borderline chimeric sequences are sequences that have a high</span>
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402
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="plaintext">enough score but which are not sufficiently different from their</span>
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403
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="plaintext">closest parent.</span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="plaintext">.TAG chimeras</span>
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404
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426
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="plaintext">.TP</span>
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405
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427
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="plaintext">.BI \-\-chimeras \0filename</span>
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406
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428
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="plaintext">Output chimeric sequences to \fIfilename\fR, in fasta format. Output</span>
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407
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429
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="plaintext">order may vary when using multiple threads.</span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="plaintext">.TAG db</span>
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408
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431
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="plaintext">.TP</span>
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432
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="plaintext">.BI \-\-db \0filename</span>
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410
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="plaintext">When using \-\-uchime_ref, detect chimeras using the fasta-formatted</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">@@ -412,41 +435,50 @@ reference sequences contained in \fIfilename\fR. Reference sequences</td>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="plaintext">are assumed to be chimera-free. Chimeras cannot be detected if their</span>
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413
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436
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="plaintext">parents, or sufficiently close relatives, are not present in the</span>
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414
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437
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="plaintext">database.</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="plaintext">.TAG dn</span>
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415
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439
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="plaintext">.TP</span>
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416
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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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417
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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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418
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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="LC443" class="line" lang="plaintext">.TAG fasta_score</span>
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444
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="plaintext">.TP</span>
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445
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="plaintext">.B \-\-fasta_score</span>
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446
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="plaintext">Add the chimera score to the headers in the fasta output files for</span>
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447
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="plaintext">chimeras, non-chimeras and borderline sequences, using the format</span>
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448
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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="LC449" class="line" lang="plaintext">.TAG mindiffs</span>
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450
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="plaintext">.TP</span>
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425
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451
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="plaintext">.BI \-\-mindiffs\~ "positive integer"</span>
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426
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452
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="plaintext">Minimum number of differences per segment (default value is 3). The</span>
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427
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453
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="plaintext">parameter is ignored with \-\-uchime2_denovo and \-\-uchime3_denovo.</span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="plaintext">.TAG mindiv</span>
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428
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455
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="plaintext">.TP</span>
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429
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456
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="plaintext">.BI \-\-mindiv \0real</span>
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430
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457
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="plaintext">Minimum divergence from closest parent (default value is 0.8). The</span>
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431
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458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="plaintext">parameter is ignored with \-\-uchime2_denovo and \-\-uchime3_denovo.</span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext">.TAG minh</span>
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432
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460
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="plaintext">.TP</span>
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433
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461
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="plaintext">.BI \-\-minh \0real</span>
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434
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462
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="plaintext">Minimum score (\fIh\fR). Increasing this value tends to reduce the</span>
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435
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463
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="plaintext">number of false positives and to decrease sensitivity. Default value</span>
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436
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464
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="plaintext">is 0.28, and values ranging from 0.0 to 1.0 included are accepted. The</span>
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437
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465
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="plaintext">parameter is ignored with \-\-uchime2_denovo and \-\-uchime3_denovo.</span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext">.TAG nonchimeras</span>
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438
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467
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="plaintext">.TP</span>
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439
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468
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="plaintext">.BI \-\-nonchimeras \0filename</span>
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440
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469
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="plaintext">Output non-chimeric sequences to \fIfilename\fR, in fasta</span>
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441
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470
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="plaintext">format. Output order may vary when using multiple threads.</span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="plaintext">.TAG relabel</span>
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442
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472
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="plaintext">.TP</span>
</pre>
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443
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473
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="plaintext">.BI \-\-relabel \0string</span>
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444
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474
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="plaintext">Relabel sequences using the prefix \fIstring\fR and a ticker (1, 2, 3,</span>
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445
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475
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="plaintext">etc.) to construct the new headers. Use \-\-sizeout to conserve the</span>
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446
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476
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="plaintext">abundance annotations.</span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext">.TAG relabel_keep</span>
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447
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478
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="plaintext">.TP</span>
</pre>
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448
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479
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="plaintext">.B \-\-relabel_keep</span>
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449
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<td class="diff-line-num new_line" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
480
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="plaintext">When relabelling, keep the old identifier in the header after a space.</span>
</pre>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext">.TAG relabel_md5</span>
</pre>
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450
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482
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="plaintext">.TP</span>
</pre>
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451
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<td class="diff-line-num new_line" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
483
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="plaintext">.B \-\-relabel_md5</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
452
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<td class="diff-line-num new_line" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
484
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC484" class="line" lang="plaintext">Relabel sequences using the MD5 message digest algorithm applied to</span>
</pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -461,6 +493,11 @@ generates a 128-bit (16-byte) digest that is represented by 16</td>
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461
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493
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="plaintext">hexadecimal numbers (using 32 symbols among 0123456789abcdef). Use</span>
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462
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494
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="plaintext">\-\-sizeout to conserve the abundance annotations.</span>
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495
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="plaintext">.\" The probablity of collision for two sequences is 1/2^128</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext">.TAG relabel_self</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext">.TP</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="plaintext">.B \-\-relabel_self</span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="plaintext">Relabel sequences using each sequence itself as a label.</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="plaintext">.TAG relabel_sha1</span>
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464
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501
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="plaintext">.TP</span>
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="plaintext">.B \-\-relabel_sha1</span>
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466
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="plaintext">Relabel sequences using the SHA1 message digest algorithm applied to</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">@@ -471,27 +508,32 @@ the SHA1 algorithm instead of the MD5 algorithm. SHA1 generates a</td>
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471
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="plaintext">sequences resulting in the same digest) is smaller for the SHA1</span>
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472
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509
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="plaintext">algorithm than it is for the MD5 algorithm.</span>
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473
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510
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="plaintext">.\" The probablity of collision for two sequences is 1/2^160</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="plaintext">.TAG self</span>
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474
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="plaintext">.TP</span>
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="plaintext">.B \-\-self</span>
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="plaintext">When using \-\-uchime_ref, ignore a reference sequence when its label</span>
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477
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515
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="plaintext">matches the label of the query sequence (useful to estimate</span>
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478
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516
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="plaintext">false-positive rate in reference sequences).</span>
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479
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517
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="plaintext">.\" I am not sure the statement above is true.</span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="plaintext">.TAG selfid</span>
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480
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519
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="plaintext">.TP</span>
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481
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520
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="plaintext">.B \-\-selfid</span>
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482
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521
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="plaintext">When using \-\-uchime_ref, ignore a reference sequence when its</span>
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483
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522
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="plaintext">nucleotide sequence is strictly identical to the nucleotidic sequence</span>
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484
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523
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="plaintext">of the query.</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="plaintext">.TAG sizeout</span>
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485
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525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="plaintext">.TP</span>
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486
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="plaintext">.B \-\-sizeout</span>
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487
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<td class="diff-line-num new_line" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="plaintext">When relabelling, add abundance annotations to fasta headers (using</span>
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488
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<td class="diff-line-num new_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
528
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="plaintext">the format ';size=\fIinteger\fR;').</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="plaintext">.TAG uchime_denovo</span>
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<td class="diff-line-num old_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
489
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530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
490
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531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="plaintext">.BI \-\-uchime_denovo \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
491
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<td class="diff-line-num new_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="plaintext">Detect chimeras present in the fasta-formatted \fIfilename\fR, without</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
492
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<td class="diff-line-num new_line" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="plaintext">external references (i.e. \fIde novo\fR). Automatically sort the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
493
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534
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="plaintext">sequences in \fIfilename\fR by decreasing abundance beforehand (see</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
494
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<td class="diff-line-num new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
535
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="plaintext">the sorting section for details). Multithreading is not supported.</span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="plaintext">.TAG uchime2_denovo</span>
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<td class="diff-line-num old_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
495
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<td class="diff-line-num new_line" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
537
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="plaintext">.TP</span>
</pre>
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496
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<td class="diff-line-num new_line" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="plaintext">.BI \-\-uchime2_denovo \0filename</span>
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497
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="plaintext">Detect chimeras present in the fasta-formatted \fIfilename\fR, using</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="499" style="width: 35px; color: rgba(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="541" style="width: 35px; color: rgba(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">@@ -499,17 +541,20 @@ the UCHIME2 algorithm. This algorithm is designed for denoised</td>
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499
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="plaintext">amplicons (see \-\-cluster_unoise). Automatically sort the sequences</span>
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<td class="diff-line-num old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
500
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<td class="diff-line-num new_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
542
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="plaintext">in \fIfilename\fR by decreasing abundance beforehand (see the sorting</span>
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501
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="plaintext">section for details). Multithreading is not supported.</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="plaintext">.TAG uchime3_denovo</span>
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<td class="diff-line-num old_line" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
502
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545
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
503
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546
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="plaintext">.BI \-\-uchime3_denovo \0filename</span>
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504
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<td class="diff-line-num new_line" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
547
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="plaintext">Detect chimeras present in the fasta-formatted \fIfilename\fR, using</span>
</pre>
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505
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548
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="plaintext">the UCHIME2 algorithm. The only difference from \-\-uchime2_denovo is</span>
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506
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549
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="plaintext">that the default minimum abundance skew (\-\-abskew) is set to 16.0</span>
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507
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550
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="plaintext">rather than 2.0.</span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="plaintext">.TAG uchime_ref</span>
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508
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552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="plaintext">.TP</span>
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509
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553
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="plaintext">.BI \-\-uchime_ref \0filename</span>
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510
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554
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="plaintext">Detect chimeras present in the fasta-formatted \fIfilename\fR by</span>
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511
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555
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="plaintext">comparing them with reference sequences (option</span>
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512
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556
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="plaintext">\-\-db). Multithreading is supported.</span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="plaintext">.TAG uchimealns</span>
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513
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="plaintext">.TP</span>
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514
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="plaintext">.BI \-\-uchimealns \0filename</span>
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515
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="plaintext">Write the three-way global alignments (parentA, parentB, chimera) to</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="517" style="width: 35px; color: rgba(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="562" style="width: 35px; color: rgba(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">@@ -517,6 +562,7 @@ Write the three-way global alignments (parentA, parentB, chimera) to</td>
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517
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562
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="plaintext">modify alignment length. Output order may vary when using multiple</span>
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518
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="plaintext">threads. All sequences are converted to upper case before</span>
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519
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="plaintext">alignment. Lower case letters indicate disagreement in the alignment.</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="plaintext">.TAG uchimeout</span>
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520
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566
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="plaintext">.TP</span>
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521
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567
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="plaintext">.BI \-\-uchimeout \0filename</span>
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522
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="plaintext">Write chimera detection results to \fIfilename\fR using a 18-field,</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="566" style="width: 35px; color: rgba(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="612" style="width: 35px; color: rgba(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">@@ -566,16 +612,19 @@ div: divergence, defined as (idQM - idQT).</td>
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566
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="plaintext">YN: query is chimeric (Y), or not (N), or is a borderline case (?).</span>
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567
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="plaintext">.RE</span>
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568
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="plaintext">.RE</span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="plaintext">.TAG uchimeout5</span>
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569
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616
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="plaintext">.TP</span>
</pre>
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570
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617
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="plaintext">.B \-\-uchimeout5</span>
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571
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618
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="plaintext">When using \-\-uchimeout, write chimera detection results using a</span>
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572
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619
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="plaintext">17\-field, tab\-separated uchime\-like format (drop the 5th field of</span>
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573
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620
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="plaintext">\-\-uchimeout), compatible with usearch version 5 and earlier</span>
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574
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621
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="plaintext">versions.</span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="plaintext">.TAG xn</span>
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575
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623
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="plaintext">.TP</span>
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576
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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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577
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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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578
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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>
</pre>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="plaintext">.TAG xsize</span>
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579
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628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="plaintext">.TP</span>
</pre>
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580
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<td class="diff-line-num new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="plaintext">.B \-\-xsize</span>
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581
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630
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="plaintext">Strip abundance information from the headers when writing the output</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="583" style="width: 35px; color: rgba(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="632" style="width: 35px; color: rgba(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">@@ -583,6 +632,7 @@ file.</td>
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583
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632
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="plaintext">.RE</span>
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<td class="diff-line-num old_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
584
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633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="plaintext">.PP</span>
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585
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="plaintext">.TAG clustering-options</span>
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<td class="diff-line-num old_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
586
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636
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="plaintext">Clustering options:</span>
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587
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637
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="plaintext">.RS</span>
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588
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638
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="594" style="width: 35px; color: rgba(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="644" style="width: 35px; color: rgba(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">@@ -594,11 +644,13 @@ definition (\-\-iddef).</td>
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594
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644
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="plaintext">.PP</span>
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595
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645
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<pre style="margin: 0;"> <span id="LC645" class="line" lang="plaintext">Input sequences are masked as specified with the \-\-qmask and</span>
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596
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646
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="plaintext">\-\-hardmask options.</span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="plaintext">.TAG biomout</span>
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648
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="plaintext">.TP 9</span>
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598
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649
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="plaintext">.BI \-\-biomout \0filename</span>
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599
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650
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="plaintext">Generate an OTU table in the biom version 1.0 JSON file format as</span>
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600
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651
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="plaintext">specified at</span>
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601
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="plaintext">http://biom-format.org/documentation/format_versions/biom-1.0.html.</span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="plaintext">.URL http://biom-format.org/documentation/format_versions/biom-1.0.html "(link)"</span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="plaintext"><http://biom-format.org/documentation/format_versions/biom-1.0.html>.</span>
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602
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654
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="plaintext">The format describes how to store a sparse matrix containing the</span>
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603
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655
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="plaintext">abundances of the OTUs in the different samples. This format is much</span>
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604
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656
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="plaintext">more efficient than the classic and mothur OTU table formats available</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="674" style="width: 35px; color: rgba(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">@@ -622,42 +674,51 @@ header. The OTU identifier may contain any printable character except</td>
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622
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674
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="plaintext">semicolons. If no such OTU label is found, the identifier in the</span>
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623
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675
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="plaintext">initial part of the header will be used, and all characters except</span>
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624
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676
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="plaintext">semicolons are allowed. Alternatively, OTU identifers can be generated</span>
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625
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="plaintext">using the relabelling options (\-\-relabel, \-\-relabel_sha1 or</span>
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626
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="plaintext">\-\-relabel_md5). Taxonomy information, if present, will also be</span>
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627
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="plaintext">extracted from the headers of the centroid sequences. If the header</span>
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628
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="plaintext">contains ';tax=Homo_sapiens;' or a similar string somewhere, then the</span>
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<td class="diff-line-num old old_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
629
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="plaintext">given taxonomy information (here 'Homo_sapiens') will be used. The</span>
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630
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="plaintext">semicolon is not mandatory at the beginning or end of the header. The</span>
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<td class="diff-line-num old old_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
631
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="plaintext">taxonomy information may contain any printable character except</span>
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632
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="plaintext">semicolons. If an OTU table in the biom version 2.1 HDF5 file format</span>
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633
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="plaintext">is required, the biom utility may be used as described at</span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="plaintext">http://biom-format.org/documentation/biom_conversion.html.</span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="plaintext">using the relabelling options (\-\-relabel, \-\-relabel_self,</span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="plaintext">\-\-relabel_sha1, or \-\-relabel_md5). Taxonomy information, if</span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="plaintext">present, will also be extracted from the headers of the centroid</span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="plaintext">sequences. If the header contains ';tax=Homo_sapiens;' or a similar</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="plaintext">string somewhere, then the given taxonomy information</span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="plaintext">(here 'Homo_sapiens') will be used. The semicolon is not mandatory at</span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="plaintext">the beginning or end of the header. The taxonomy information may</span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="plaintext">contain any printable character except semicolons. If an OTU table in</span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="plaintext">the biom version 2.1 HDF5 file format is required, the biom utility</span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="plaintext">may be used as described at</span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="plaintext">.URL http://biom-format.org/documentation/biom_conversion.html "(link)"</span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="plaintext"><http://biom-format.org/documentation/biom_conversion.html>.</span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="plaintext">.TAG centroids</span>
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635
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690
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="plaintext">.TP</span>
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636
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691
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="plaintext">.BI \-\-centroids \0filename</span>
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637
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692
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="plaintext">Output cluster centroid sequences to \fIfilename\fR, in fasta</span>
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638
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693
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="plaintext">format. The centroid is the sequence that seeded the cluster (i.e. the</span>
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639
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694
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="plaintext">first sequence of the cluster).</span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="plaintext">.TAG clusterout_id</span>
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640
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696
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="plaintext">.TP</span>
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641
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697
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="plaintext">.BI \-\-clusterout_id</span>
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642
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698
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="plaintext">Add cluster identifier information to the output files</span>
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643
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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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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="plaintext">.TAG clusterout_sort</span>
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644
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701
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="plaintext">.TP</span>
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645
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702
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="plaintext">.BI \-\-clusterout_sort</span>
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646
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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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647
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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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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="plaintext">.TAG cluster_fast</span>
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648
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706
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="plaintext">.TP</span>
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649
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707
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="plaintext">.BI \-\-cluster_fast \0filename</span>
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650
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708
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="plaintext">Clusterize the fasta sequences in \fIfilename\fR, automatically sort</span>
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651
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709
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="plaintext">by decreasing sequence length beforehand.</span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="plaintext">.TAG cluster_size</span>
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652
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711
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="plaintext">.TP</span>
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653
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712
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="plaintext">.BI \-\-cluster_size \0filename</span>
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654
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713
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="plaintext">Clusterize the fasta sequences in \fIfilename\fR, automatically sort</span>
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655
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714
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="plaintext">by decreasing sequence abundance beforehand.</span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="plaintext">.TAG cluster_smallmem</span>
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656
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="plaintext">.TP</span>
</pre>
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657
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717
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="plaintext">.BI \-\-cluster_smallmem \0filename</span>
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658
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="plaintext">Clusterize the fasta sequences in \fIfilename\fR without automatically</span>
</pre>
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659
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719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="plaintext">modifying their order beforehand. Sequence are expected to be sorted</span>
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660
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="plaintext">by decreasing sequence length, unless \-\-usersort is used.</span>
</pre>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="plaintext">.TAG cluster_unoise</span>
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661
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="plaintext">.TP</span>
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662
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723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="plaintext">.BI \-\-cluster_unoise \0filename</span>
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663
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724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="plaintext">Perform denoising of the fasta sequences in \fIfilename\fR according</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="666" style="width: 35px; color: rgba(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="727" style="width: 35px; color: rgba(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">@@ -666,11 +727,13 @@ chimera removal step. The options \-\-minsize (default 8) and</td>
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666
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727
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="plaintext">\-\-unoise_alpha (default 2.0) may be specified. Chimera removal</span>
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667
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728
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="plaintext">(\fIde novo\fR) should be performed afterwards with</span>
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668
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729
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<pre style="margin: 0;"> <span id="LC729" class="line" lang="plaintext">\-\-uchime3_denovo.</span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="plaintext">.TAG clusters</span>
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669
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731
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="plaintext">.TP</span>
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670
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732
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="plaintext">.BI \-\-clusters \0string</span>
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671
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733
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="plaintext">Output each cluster to a separate fasta file using the prefix</span>
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672
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734
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="plaintext">\fIstring\fR and a ticker (0, 1, 2, etc.) to construct the path and</span>
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673
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735
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="plaintext">filenames.</span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="plaintext">.TAG consout</span>
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674
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737
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="plaintext">.TP</span>
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675
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738
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="plaintext">.BI \-\-consout \0filename</span>
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676
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<td class="diff-line-num new_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
739
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="plaintext">Output cluster consensus sequences to \fIfilename\fR. For each</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="679" style="width: 35px; color: rgba(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="742" style="width: 35px; color: rgba(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">@@ -679,6 +742,7 @@ constructed by taking the majority symbol (nucleotide or gap) from</td>
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679
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742
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="plaintext">each column of the alignment. Columns containing a majority of gaps</span>
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680
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<td class="diff-line-num new_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
743
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<pre style="margin: 0;"> <span id="LC743" class="line" lang="plaintext">are skipped, except for terminal gaps. If the \-\-sizein</span>
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681
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744
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="plaintext">option is specified, sequence abundances will be taken into account.</span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="plaintext">.TAG cons_truncate</span>
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682
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746
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="plaintext">.TP</span>
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683
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747
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="plaintext">.B \-\-cons_truncate</span>
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684
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748
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="plaintext">This command is ignored. A warning is issued.</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="752" style="width: 35px; color: rgba(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">@@ -688,6 +752,7 @@ This command is ignored. A warning is issued.</td>
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688
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752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="plaintext">.\" do not ignore terminal gaps. That option skips terminal columns</span>
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689
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753
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="plaintext">.\" if they contain a majority of gaps, yielding shorter consensus</span>
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690
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754
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="plaintext">.\" sequences than when using \-\-consout alone.</span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="plaintext">.TAG id</span>
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691
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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="plaintext">.TP</span>
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692
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="plaintext">.BI \-\-id \0real</span>
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693
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="plaintext">Do not add the target to the cluster if the pairwise identity with the</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="695" style="width: 35px; color: rgba(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">@@ -695,6 +760,7 @@ centroid is lower than \fIreal\fR (value ranging from 0.0 to 1.0</td>
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695
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="plaintext">included). The pairwise identity is defined as the number of (matching</span>
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696
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="plaintext">columns) / (alignment length - terminal gaps). That definition can be</span>
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697
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="plaintext">modified by \-\-iddef.</span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="plaintext">.TAG iddef</span>
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698
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="plaintext">.TP</span>
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699
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="plaintext">.BI \-\-iddef\~ "0|1|2|3|4"</span>
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700
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="plaintext">Change the pairwise identity definition used in \-\-id. Values</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="718" style="width: 35px; color: rgba(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">@@ -718,10 +784,12 @@ BLAST definition, equivalent to \-\-iddef 1 in a context of global</td>
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718
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784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="plaintext">pairwise alignment.</span>
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719
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="plaintext">.RE</span>
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720
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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="plaintext">.RE</span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="plaintext">.TAG minsize</span>
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<td class="diff-line-num old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
721
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="plaintext">.TP</span>
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722
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="plaintext">.BI \-\-minsize\~ "positive integer"</span>
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<td class="diff-line-num old_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
723
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<td class="diff-line-num new_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="plaintext">Specify the minimum abundance of sequences for denoising using</span>
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724
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="plaintext">\-\-cluster_unoise. The default is 8.</span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="plaintext">.TAG msaout</span>
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725
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793
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="plaintext">.TP</span>
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726
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794
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="plaintext">.BI \-\-msaout \0filename</span>
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727
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<td class="diff-line-num new_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
795
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="plaintext">Output a multiple sequence alignment and a consensus sequence for each</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="733" style="width: 35px; color: rgba(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="801" style="width: 35px; color: rgba(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">@@ -733,10 +801,13 @@ the majority symbol (nucleotide or gap) from each column of the</td>
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733
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801
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="plaintext">alignment. Columns containing a majority of gaps are skipped, except</span>
</pre>
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734
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802
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="plaintext">for terminal gaps. If the \-\-sizein option is specified, sequence</span>
</pre>
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735
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803
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="plaintext">abundances will be taken into account when computing the consensus.</span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="plaintext">.TAG mothur_shared_out</span>
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736
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<td class="diff-line-num new_line" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
805
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="plaintext">.TP</span>
</pre>
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737
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<td class="diff-line-num new_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="plaintext">.BI \-\-mothur_shared_out \0filename</span>
</pre>
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738
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807
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="plaintext">Output an OTU table in the mothur 'shared' tab-separated plain text</span>
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739
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<td class="diff-line-num new_line old" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC739" class="line" lang="plaintext">format as described at http://www.mothur.org/wiki/Shared_file. The</span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="plaintext">format as described at</span>
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<td class="diff-line-num new new_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="plaintext">.URL https://www.mothur.org/wiki/Shared_file (link)</span>
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<td class="diff-line-num new new_line" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="plaintext"><https://www.mothur.org/wiki/Shared_file>. The</span>
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740
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<td class="diff-line-num new_line" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="plaintext">format describes how a matrix containing the abundances of the OTUs in</span>
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<td class="diff-line-num old_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
741
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<td class="diff-line-num new_line" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="plaintext">the different samples is stored. The first line will start with the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
742
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<td class="diff-line-num new_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="plaintext">strings 'label', 'group' and 'numOtus' and is followed by a list of</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="747" style="width: 35px; color: rgba(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="818" style="width: 35px; color: rgba(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">@@ -747,6 +818,7 @@ in the order given on the first line. The OTU and sample identifiers</td>
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<td class="diff-line-num old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
747
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<td class="diff-line-num new_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
818
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="plaintext">are extracted from the FASTA headers of the sequences. The OTUs are</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
748
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<td class="diff-line-num new_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="plaintext">represented by the cluster centroids. See the \-\-biomout option for</span>
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<td class="diff-line-num old_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
749
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<td class="diff-line-num new_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="plaintext">further details.</span>
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<td class="diff-line-num new new_line" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="plaintext">.TAG otutabout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
750
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<td class="diff-line-num new_line" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
822
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
751
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<td class="diff-line-num new_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
823
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="plaintext">.BI \-\-otutabout \0filename</span>
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752
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<td class="diff-line-num new_line" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
824
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="plaintext">Output an OTU table in the classic tab-separated plain text format as</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="762" style="width: 35px; color: rgba(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="834" style="width: 35px; color: rgba(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">@@ -762,6 +834,7 @@ added to the right of the table if taxonomy information is available</td>
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<td class="diff-line-num old_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
762
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<td class="diff-line-num new_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
834
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="plaintext">for at least one of the OTUs. This column will be labelled 'taxonomy'</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
763
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<td class="diff-line-num new_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="plaintext">and each row will then contain the taxonomy information extracted for</span>
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<td class="diff-line-num old_line" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
764
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<td class="diff-line-num new_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="plaintext">that OTU. See the \-\-biomout option for further details.</span>
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</td>
<td class="diff-line-num new new_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="plaintext">.TAG profile</span>
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765
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<td class="diff-line-num new_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
838
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
766
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<td class="diff-line-num new_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
839
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<pre style="margin: 0;"> <span id="LC839" class="line" lang="plaintext">.BI \-\-profile \0filename</span>
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767
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<td class="diff-line-num new_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
840
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="plaintext">Output a sequence profile to a text file with the frequency of each</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="773" style="width: 35px; color: rgba(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="846" style="width: 35px; color: rgba(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">@@ -773,35 +846,48 @@ number of Cs, number of Gs, number of Ts or Us, number of gap symbols,</td>
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<td class="diff-line-num old_line" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
773
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<td class="diff-line-num new_line" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
846
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<pre style="margin: 0;"> <span id="LC846" class="line" lang="plaintext">and finally the total number of ambiguous nucleotide symbols (B, D, H,</span>
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<td class="diff-line-num old_line" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
774
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<td class="diff-line-num new_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
847
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<pre style="margin: 0;"> <span id="LC847" class="line" lang="plaintext">K, M, N, R, S, Y, V or W). All numbers are integers. If the \-\-sizein</span>
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775
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<td class="diff-line-num new_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
848
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<pre style="margin: 0;"> <span id="LC848" class="line" lang="plaintext">option is specified, sequence abundances will be taken into account.</span>
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<td class="diff-line-num new new_line" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="plaintext">.TAG qmask</span>
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<td class="diff-line-num old_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
776
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<td class="diff-line-num new_line" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
777
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<td class="diff-line-num new_line" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
851
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="plaintext">.BI \-\-qmask\~ "none|dust|soft"</span>
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<td class="diff-line-num old_line" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
778
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<td class="diff-line-num new_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="plaintext">Mask regions in sequences using the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
779
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<td class="diff-line-num new_line" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
853
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<pre style="margin: 0;"> <span id="LC853" class="line" lang="plaintext">\fIdust\fR or the \fIsoft\fR methods, or do not mask</span>
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<td class="diff-line-num 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">
780
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<td class="diff-line-num new_line" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
854
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="plaintext">(\fInone\fR). Warning, when using \fIsoft\fR masking, clustering</span>
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<td class="diff-line-num old_line" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
781
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<td class="diff-line-num new_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="plaintext">becomes case sensitive. The default is to mask using \fIdust\fR.</span>
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<td class="diff-line-num new old_line" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); 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="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="plaintext">.TAG relabel</span>
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<td class="diff-line-num 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">
782
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<td class="diff-line-num new_line" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
857
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<pre style="margin: 0;"> <span id="LC857" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
783
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<td class="diff-line-num new_line" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="plaintext">.BI \-\-relabel \0string</span>
</pre>
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<td class="diff-line-num old_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">
784
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<td class="diff-line-num new_line" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="plaintext">Relabel sequence identifiers in the output files produced by</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
785
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<td class="diff-line-num new_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
860
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="plaintext">\-\-consout, \-\-profile and \-\-centroids options. Please see the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
786
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<td class="diff-line-num new_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
861
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="plaintext">description of the same option under Chimera detection for details.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); 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="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="plaintext">.TAG relabel_keep</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
787
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<td class="diff-line-num new_line" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
863
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
788
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<td class="diff-line-num new_line" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="plaintext">.B \-\-relabel_keep</span>
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<td class="diff-line-num old_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
789
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<td class="diff-line-num new_line" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="plaintext">When relabelling, keep the old identifier in the header after a space.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="plaintext">.TAG relabel_md5</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
790
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<td class="diff-line-num new_line" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
867
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC867" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
791
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<td class="diff-line-num new_line old" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC791" class="line" lang="plaintext">.B<span class="idiff left right">I</span> \-\-relabel_md5</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="plaintext">.B \-\-relabel_md5</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
792
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<td class="diff-line-num new_line" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
869
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC869" class="line" lang="plaintext">Relabel sequence identifiers in the output files produced by</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
793
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<td class="diff-line-num new_line" data-linenumber="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
870
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC870" class="line" lang="plaintext">\-\-consout, \-\-profile and \-\-centroids options. Please see the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
794
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<td class="diff-line-num new_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
871
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC871" class="line" lang="plaintext">description of the same option under Chimera detection for details.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="plaintext">.TAG relabel_self</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
795
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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="plaintext">.TP</span>
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796
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<pre style="margin: 0;">-<span id="LC796" class="line" lang="plaintext">.B<span class="idiff left right">I \-\-relabel_sha1</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="plaintext">.B<span class="idiff left right"> \-\-relabel_self</span></span>
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797
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875
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<pre style="margin: 0;"> <span id="LC875" class="line" lang="plaintext">Relabel sequence identifiers in the output files produced by</span>
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798
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876
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="plaintext">\-\-consout, \-\-profile and \-\-centroids options. Please see the</span>
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799
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877
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="plaintext">description of the same option under Chimera detection for details.</span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="plaintext">.TAG relabel_sha1</span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="plaintext">.TP</span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="plaintext">.B \-\-relabel_sha1</span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="plaintext">Relabel sequence identifiers in the output files produced by</span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="plaintext">\-\-consout, \-\-profile and \-\-centroids options. Please see the</span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="plaintext">description of the same option under Chimera detection for details.</span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="plaintext">.TAG sizein</span>
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800
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885
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="plaintext">.TP</span>
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801
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886
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="plaintext">.B \-\-sizein</span>
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802
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887
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="plaintext">Take into account the abundance annotations present in the input fasta</span>
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803
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888
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="plaintext">file (search for the pattern '[>;]size=\fIinteger\fR[;]' in sequence</span>
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804
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889
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="plaintext">headers).</span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="plaintext">.TAG sizeorder</span>
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805
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891
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<pre style="margin: 0;"> <span id="LC891" class="line" lang="plaintext">.TP</span>
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806
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892
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<pre style="margin: 0;"> <span id="LC892" class="line" lang="plaintext">.B \-\-sizeorder</span>
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807
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893
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<pre style="margin: 0;"> <span id="LC893" class="line" lang="plaintext">When an amplicon is close to 2 or more centroids, both within the</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="812" style="width: 35px; color: rgba(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">@@ -812,6 +898,7 @@ specified with \-\-maxaccepts is higher than one. The \-\-sizeorder</td>
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812
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898
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<pre style="margin: 0;"> <span id="LC898" class="line" lang="plaintext">option turns on what is sometimes referred to as abundance-based</span>
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813
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899
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="plaintext">greedy clustering (AGC), in contrast to the default distance-based</span>
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814
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900
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="plaintext">greedy clustering (DGC).</span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="plaintext">.TAG sizeout</span>
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815
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902
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="plaintext">.TP</span>
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816
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903
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<pre style="margin: 0;"> <span id="LC903" class="line" lang="plaintext">.B \-\-sizeout</span>
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817
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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 pattern</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="909" style="width: 35px; color: rgba(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">@@ -822,10 +909,12 @@ the total abundance of the amplicons included in the cluster</td>
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822
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909
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="plaintext">(\-\-centroids option). If \-\-sizein is not specified, input</span>
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<td class="diff-line-num old_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
823
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<td class="diff-line-num new_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
910
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="plaintext">abundances are set to 1 for amplicons, and to the number of amplicons</span>
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<td class="diff-line-num old_line" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
824
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<td class="diff-line-num new_line" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
911
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="plaintext">per cluster for centroids.</span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="plaintext">.TAG strand</span>
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<td class="diff-line-num old_line" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
825
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<td class="diff-line-num new_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
913
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<pre style="margin: 0;"> <span id="LC913" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
826
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<td class="diff-line-num new_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">
914
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<pre style="margin: 0;"> <span id="LC914" class="line" lang="plaintext">.BI \-\-strand\~ "plus|both"</span>
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<td class="diff-line-num old_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
827
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915
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<pre style="margin: 0;"> <span id="LC915" class="line" lang="plaintext">When comparing sequences with the cluster seed, check the \fIplus\fR</span>
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<td class="diff-line-num old_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
828
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<td class="diff-line-num 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">
916
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<pre style="margin: 0;"> <span id="LC916" class="line" lang="plaintext">strand only (default) or check \fIboth\fR strands.</span>
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<td class="diff-line-num new old_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="plaintext">.TAG uc</span>
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829
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918
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<pre style="margin: 0;"> <span id="LC918" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
830
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919
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<pre style="margin: 0;"> <span id="LC919" class="line" lang="plaintext">.BI \-\-uc \0filename</span>
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831
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920
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<pre style="margin: 0;"> <span id="LC920" class="line" lang="plaintext">Output clustering results in \fIfilename\fR using a tab-separated</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="866" style="width: 35px; color: rgba(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="955" style="width: 35px; color: rgba(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">@@ -866,14 +955,17 @@ Label of the query sequence (H), or of the centroid sequence (S, C).</td>
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866
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955
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<pre style="margin: 0;"> <span id="LC955" class="line" lang="plaintext">Label of the centroid sequence (H), or set to '*' (S, C).</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
867
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956
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="plaintext">.RE</span>
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868
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957
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="plaintext">.RE</span>
</pre>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="plaintext">.TAG unoise_alpha</span>
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<td class="diff-line-num old_line" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
869
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959
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<pre style="margin: 0;"> <span id="LC959" class="line" lang="plaintext">.TP</span>
</pre>
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870
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960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="plaintext">.BI \-\-unoise_alpha\~ real</span>
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<td class="diff-line-num old_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
871
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<td class="diff-line-num new_line" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="plaintext">Specify the alpha parameter to the \-\-cluster_unoise command. The</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
872
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<td class="diff-line-num new_line" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
962
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="plaintext">default i 2.0.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="plaintext">.TAG usersort</span>
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873
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964
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<pre style="margin: 0;"> <span id="LC964" class="line" lang="plaintext">.TP</span>
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874
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965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="plaintext">.B \-\-usersort</span>
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875
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966
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<pre style="margin: 0;"> <span id="LC966" class="line" lang="plaintext">When using \-\-cluster_smallmem, allow any sequence input order, not</span>
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876
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="plaintext">just a decreasing length ordering.</span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="plaintext">.TAG xsize</span>
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877
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969
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<pre style="margin: 0;"> <span id="LC969" class="line" lang="plaintext">.TP</span>
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878
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970
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<pre style="margin: 0;"> <span id="LC970" class="line" lang="plaintext">.B \-\-xsize</span>
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879
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971
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<pre style="margin: 0;"> <span id="LC971" class="line" lang="plaintext">Strip abundance information from the headers when writing the 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">@@ -888,8 +980,10 @@ definitions): \-\-alnout, \-\-blast6out, \-\-fastapairs, \-\-matched,</td>
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888
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980
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<pre style="margin: 0;"> <span id="LC980" class="line" lang="plaintext">.RE</span>
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889
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981
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<pre style="margin: 0;"> <span id="LC981" class="line" lang="plaintext">.PP</span>
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890
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982
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<pre style="margin: 0;"> <span id="LC982" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="plaintext">.TAG dereplication-and-rereplication-options</span>
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891
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984
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<pre style="margin: 0;"> <span id="LC984" class="line" lang="plaintext">Dereplication and rereplication options:</span>
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892
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985
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<pre style="margin: 0;"> <span id="LC985" class="line" lang="plaintext">.RS</span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="plaintext">.TAG derep_fulllength</span>
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893
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987
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<pre style="margin: 0;"> <span id="LC987" class="line" lang="plaintext">.TP 9</span>
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894
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988
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<pre style="margin: 0;"> <span id="LC988" class="line" lang="plaintext">.BI \-\-derep_fulllength \0filename</span>
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895
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989
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<pre style="margin: 0;"> <span id="LC989" class="line" lang="plaintext">Merge strictly identical sequences contained in</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">@@ -898,6 +992,7 @@ length and the same string of nucleotides (case insensitive, T and U</td>
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898
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992
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="plaintext">are considered the same). See the options \-\-sizein and \-\-sizeout</span>
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899
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993
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<pre style="margin: 0;"> <span id="LC993" class="line" lang="plaintext">to take into account and compute abundance values. This command does</span>
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900
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994
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<pre style="margin: 0;"> <span id="LC994" class="line" lang="plaintext">not support multithreading.</span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="plaintext">.TAG derep_prefix</span>
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901
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996
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<pre style="margin: 0;"> <span id="LC996" class="line" lang="plaintext">.TP</span>
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902
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997
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<pre style="margin: 0;"> <span id="LC997" class="line" lang="plaintext">.BI \-\-derep_prefix \0filename</span>
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903
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998
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<pre style="margin: 0;"> <span id="LC998" class="line" lang="plaintext">Merge sequences with identical prefixes contained in \fIfilename\fR.</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="909" style="width: 35px; color: rgba(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="1004" style="width: 35px; color: rgba(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">@@ -909,14 +1004,17 @@ it is clustered with the most abundant. Remaining ties are solved</td>
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<td class="diff-line-num old_line" data-linenumber="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
909
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<td class="diff-line-num new_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1004
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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="plaintext">using sequence headers and sequence input order. Sequence comparisons</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
910
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<td class="diff-line-num new_line" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1005
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<pre style="margin: 0;"> <span id="LC1005" class="line" lang="plaintext">are case insensitive, and T and U are considered identical. This</span>
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<td class="diff-line-num old_line" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
911
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<td class="diff-line-num new_line" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1006
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<pre style="margin: 0;"> <span id="LC1006" class="line" lang="plaintext">command does not support multithreading.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); 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="1007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="plaintext">.TAG maxuniquesize</span>
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<td class="diff-line-num old_line" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
912
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<td class="diff-line-num new_line" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1008
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<pre style="margin: 0;"> <span id="LC1008" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
913
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<td class="diff-line-num new_line" data-linenumber="1009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1009
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<pre style="margin: 0;"> <span id="LC1009" class="line" lang="plaintext">.BI \-\-maxuniquesize\~ "positive integer"</span>
</pre>
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<td class="diff-line-num 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">
914
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<td class="diff-line-num 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">
1010
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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="plaintext">Discard sequences with a post-dereplication abundance value greater</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
915
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1011" class="line" lang="plaintext">than \fIinteger\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="plaintext">.TAG minuniquesize</span>
</pre>
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<td class="diff-line-num old_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">
916
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<td class="diff-line-num new_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1013
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1013" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
917
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<td class="diff-line-num new_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1014
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<pre style="margin: 0;"> <span id="LC1014" class="line" lang="plaintext">.BI \-\-minuniquesize\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
918
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<td class="diff-line-num new_line" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1015
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="plaintext">Discard sequences with a post-dereplication abundance value smaller</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
919
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<td class="diff-line-num new_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1016
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1016" class="line" lang="plaintext">than \fIinteger\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="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">.TAG output</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
920
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<td class="diff-line-num new_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1018
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1018" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
921
</td>
<td class="diff-line-num 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">
1019
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1019" class="line" lang="plaintext">.BI \-\-output \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
922
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<td class="diff-line-num new_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1020
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1020" class="line" lang="plaintext">Write the dereplicated sequences to \fIfilename\fR, in fasta format</span>
</pre>
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</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1024" style="width: 35px; color: rgba(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">@@ -926,35 +1024,47 @@ the number of occurrences (i.e. abundance) of each sequence is</td>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1024
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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 pattern</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
927
</td>
<td class="diff-line-num new_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1025
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1025" class="line" lang="plaintext">';size=\fIinteger\fR;'.</span>
</pre>
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<td class="diff-line-num old_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">
928
</td>
<td class="diff-line-num new_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
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1026" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="plaintext">.TAG relabel</span>
</pre>
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<td class="diff-line-num old_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
</td>
<td class="diff-line-num new_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1028
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1028" class="line" lang="plaintext">.BI \-\-relabel \0string</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
930
</td>
<td class="diff-line-num new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1029
</td>
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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="plaintext">Please see the description of the same option under Chimera detection</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
931
</td>
<td class="diff-line-num new_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1030
</td>
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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="plaintext">for details.</span>
</pre>
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932
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<td class="diff-line-num new_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1031
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<pre style="margin: 0;"> <span id="LC1031" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); 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="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="plaintext">.TAG relabel_keep</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
933
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<td class="diff-line-num new_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1033
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<pre style="margin: 0;"> <span id="LC1033" class="line" lang="plaintext">.B \-\-relabel_keep</span>
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<td class="diff-line-num old_line" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
934
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<td class="diff-line-num new_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1034
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<pre style="margin: 0;"> <span id="LC1034" class="line" lang="plaintext">When relabelling, keep the old identifier in the header after a space.</span>
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<td class="diff-line-num old_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
935
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<td class="diff-line-num new_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">
1035
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1035" class="line" lang="plaintext">.TP</span>
</pre>
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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="1036" style="width: 35px; color: rgba(0,0,0,0.3); 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="plaintext">.BI \-\-relabel_md5</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); 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="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1036
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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="LC1036" class="line" lang="plaintext">.TAG relabel_md5</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1037
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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="LC1037" class="line" lang="plaintext">.B \-\-relabel_md5</span>
</pre>
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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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<td class="diff-line-num new_line" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="plaintext">Please see the description of the same option under Chimera detection</span>
</pre>
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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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<td class="diff-line-num new_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1039
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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="plaintext">for details.</span>
</pre>
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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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<td class="diff-line-num new_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1040
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1040" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
940
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<td class="diff-line-num new_line old" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC940" class="line" lang="plaintext">.BI \-\-relabel_sha1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); 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="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="plaintext">.TAG relabel_self</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); 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="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1042
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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="LC1042" class="line" lang="plaintext">.B \-\-relabel_self</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); 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="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="plaintext">Please see the description of the same option under Chimera detection</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); 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="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="plaintext">for details.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); 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="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1045
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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="LC1045" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); 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="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="plaintext">.TAG relabel_sha1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); 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="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="plaintext">.B \-\-relabel_sha1</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
941
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<td class="diff-line-num new_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1048
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1048" class="line" lang="plaintext">Please see the description of the same option under Chimera detection</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
942
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<td class="diff-line-num new_line" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1049
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1049" class="line" lang="plaintext">for details.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
943
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1050" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); 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="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="plaintext">.TAG rereplicate</span>
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<td class="diff-line-num old_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
944
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<td class="diff-line-num new_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1052
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1052" class="line" lang="plaintext">.BI \-\-rereplicate \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
945
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<td class="diff-line-num new_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1053
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<pre style="margin: 0;"> <span id="LC1053" class="line" lang="plaintext">Duplicate each sequence the number of times indicated by the abundance</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
946
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<td class="diff-line-num new_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1054
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1054" class="line" lang="plaintext">of each sequence in the specified file (option \-\-sizein is always</span>
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947
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1055
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="plaintext">implied). The sequence labels are identical for the same sequence,</span>
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948
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<pre style="margin: 0;">-<span id="LC948" class="line" lang="plaintext">unless \-\-relabel, \-\-relabel_sha1 or \-\-relabel_md5 is used to</span>
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949
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<pre style="margin: 0;">-<span id="LC949" class="line" lang="plaintext">create unique labels. Output is written to the file specified with the</span>
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950
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<pre style="margin: 0;">-<span id="LC950" class="line" lang="plaintext">\-\-output option, in FASTA format. The output file does not contain</span>
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951
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<pre style="margin: 0;">-<span id="LC951" class="line" lang="plaintext">abundance information unless \-\-sizeout is specified, in which case</span>
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952
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<pre style="margin: 0;">-<span id="LC952" class="line" lang="plaintext">an abundance of 1 is used.</span>
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1056
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<pre style="margin: 0;">+<span id="LC1056" class="line" lang="plaintext">unless \-\-relabel, \-\-relabel_self, \-\-relabel_sha1 or</span>
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1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="plaintext">\-\-relabel_md5 is used to create unique labels. Output is written to</span>
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1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="plaintext">the file specified with the \-\-output option, in FASTA format. The</span>
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1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="plaintext">output file does not contain abundance information unless \-\-sizeout</span>
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="plaintext">is specified, in which case an abundance of 1 is used.</span>
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1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="plaintext">.TAG sizein</span>
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953
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1062
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<pre style="margin: 0;"> <span id="LC1062" class="line" lang="plaintext">.TP</span>
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954
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1063
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="plaintext">.B \-\-sizein</span>
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955
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1064
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<pre style="margin: 0;"> <span id="LC1064" class="line" lang="plaintext">Take into account the abundance annotations present in the input fasta</span>
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956
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1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="plaintext">file (search for the pattern '[>;]size=\fIinteger\fR[;]' in sequence</span>
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957
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1066
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<pre style="margin: 0;"> <span id="LC1066" class="line" lang="plaintext">headers). That option is active by default when rereplicating.</span>
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1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="plaintext">.TAG sizeout</span>
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958
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1068
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<pre style="margin: 0;"> <span id="LC1068" class="line" lang="plaintext">.TP</span>
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959
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1069
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<pre style="margin: 0;"> <span id="LC1069" class="line" lang="plaintext">.B \-\-sizeout</span>
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960
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1070
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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 pattern</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="964" style="width: 35px; color: rgba(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="1074" style="width: 35px; color: rgba(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">@@ -964,13 +1074,16 @@ corresponding to its total abundance (sum of the abundances of its</td>
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964
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1074
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<pre style="margin: 0;"> <span id="LC1074" class="line" lang="plaintext">occurrences). If \-\-sizein is not specified, input abundances are set</span>
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965
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1075
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<pre style="margin: 0;"> <span id="LC1075" class="line" lang="plaintext">to 1, and each unique sequence receives a new abundance value</span>
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966
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1076
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<pre style="margin: 0;"> <span id="LC1076" class="line" lang="plaintext">corresponding to its number of occurrences in the input file.</span>
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1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="plaintext">.TAG strand</span>
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<td class="diff-line-num old_line" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
967
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<td class="diff-line-num new_line" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1078
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<pre style="margin: 0;"> <span id="LC1078" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
968
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<td class="diff-line-num new_line" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1079
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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="plaintext">.BI \-\-strand\~ "plus|both"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
969
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<td class="diff-line-num new_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1080
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<pre style="margin: 0;"> <span id="LC1080" class="line" lang="plaintext">When searching for strictly identical sequences, check the \fIplus\fR</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
970
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<td class="diff-line-num new_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1081
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<pre style="margin: 0;"> <span id="LC1081" class="line" lang="plaintext">strand only (default) or check \fIboth\fR strands.</span>
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<td class="diff-line-num new old_line" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); 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="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="plaintext">.TAG topn</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
971
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<td class="diff-line-num new_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1083
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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
972
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<td class="diff-line-num new_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1084
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<pre style="margin: 0;"> <span id="LC1084" class="line" lang="plaintext">.BI \-\-topn\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_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">
973
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<td class="diff-line-num new_line" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1085
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1085" class="line" lang="plaintext">Output only the top \fIinteger\fR sequences (i.e. the most abundant).</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="plaintext">.TAG uc</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
974
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<td class="diff-line-num new_line" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1087
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<pre style="margin: 0;"> <span id="LC1087" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
975
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<td class="diff-line-num new_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1088
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<pre style="margin: 0;"> <span id="LC1088" class="line" lang="plaintext">.BI \-\-uc \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
976
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<td class="diff-line-num new_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1089
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1089" class="line" lang="plaintext">Output full-length or prefix-dereplication results in \fIfilename\fR</span>
</pre>
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</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1007" style="width: 35px; color: rgba(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="1120" style="width: 35px; color: rgba(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">@@ -1007,13 +1120,17 @@ Label of the query sequence (H), or of the centroid sequence (S, C).</td>
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<td class="diff-line-num old_line" data-linenumber="1007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1007
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<td class="diff-line-num new_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1120
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1120" class="line" lang="plaintext">Label of the centroid sequence (H), or set to '*' (S, C).</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1008
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<td class="diff-line-num new_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="plaintext">.RE</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1009
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<td class="diff-line-num new_line" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1122
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<pre style="margin: 0;"> <span id="LC1122" class="line" lang="plaintext">.RE</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="plaintext">.RE</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="plaintext">.RS</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="plaintext">.TAG xsize</span>
</pre>
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<td class="diff-line-num old_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">
1010
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<td class="diff-line-num new_line" data-linenumber="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1127
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1127" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1128
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="plaintext">.B \-\-xsize</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1012
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<td class="diff-line-num new_line old" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1012" class="line" lang="plaintext">Strip abundance information from the headers when writing the output</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1013
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<td class="diff-line-num new_line old" data-linenumber="1129" style="width: 35px; color: rgba(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="LC1013" class="line" lang="plaintext">file.</span>
</pre>
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<td class="diff-line-num new old_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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="plaintext">Strip abundance information from the headers when writing the output file.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1014
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<td class="diff-line-num new_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1130
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<pre style="margin: 0;"> <span id="LC1130" class="line" lang="plaintext">.RE</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1015
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1131
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<pre style="margin: 0;"> <span id="LC1131" class="line" lang="plaintext">.PP</span>
</pre>
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1016
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1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="plaintext">.TAG extraction-options</span>
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<td class="diff-line-num old_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1017
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<td class="diff-line-num new_line" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1134
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="plaintext">Extraction options:</span>
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<td class="diff-line-num old_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1018
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<td class="diff-line-num new_line" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1135
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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="plaintext">.RS</span>
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<td class="diff-line-num old_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">
1019
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<td class="diff-line-num new_line" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1136
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<pre style="margin: 0;"> <span id="LC1136" class="line" lang="plaintext">.PP</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1056" style="width: 35px; color: rgba(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="1173" style="width: 35px; color: rgba(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">@@ -1056,20 +1173,24 @@ beginning or end of the header. Word matching is case-sensitive. The</td>
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<td class="diff-line-num old_line" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1056
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<td class="diff-line-num new_line" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1173
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<pre style="margin: 0;"> <span id="LC1173" class="line" lang="plaintext">\-\-label_field option will limit the matching of words to a certain</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1057
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<td class="diff-line-num new_line" data-linenumber="1174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1174
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<pre style="margin: 0;"> <span id="LC1174" class="line" lang="plaintext">field in the header.</span>
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<td class="diff-line-num old_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1058
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<td class="diff-line-num new_line" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1175
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<pre style="margin: 0;"> <span id="LC1175" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="plaintext">.TAG fastaout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1059
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<td class="diff-line-num new_line" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1177
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<pre style="margin: 0;"> <span id="LC1177" class="line" lang="plaintext">.TP 9</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1060
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<td class="diff-line-num new_line" data-linenumber="1178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1178
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1178" class="line" lang="plaintext">.BI \-\-fastaout \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1061
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<td class="diff-line-num new_line" data-linenumber="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1179
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1179" class="line" lang="plaintext">Write the extracted sequences in FASTA format to the file with the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1062
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<td class="diff-line-num new_line" data-linenumber="1180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1180
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1180" class="line" lang="plaintext">given name.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); 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="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="plaintext">.TAG fastqout</span>
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<td class="diff-line-num old_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1063
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<td class="diff-line-num new_line" data-linenumber="1182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1182
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1182" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1064
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<td class="diff-line-num new_line" data-linenumber="1183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1183
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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="plaintext">.BI \-\-fastqout \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1065
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<td class="diff-line-num new_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1184
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1184" class="line" lang="plaintext">Write the extracted sequences in FASTQ format to the file with the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1066
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<td class="diff-line-num new_line" data-linenumber="1185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1185
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1185" class="line" lang="plaintext">given name. This option is illegal if the input is in FASTA format.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); 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="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="plaintext">.TAG fastx_getseq</span>
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<td class="diff-line-num old_line" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1067
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<td class="diff-line-num new_line" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1187
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1187" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1068
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<td class="diff-line-num new_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1188
</td>
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<pre style="margin: 0;"> <span id="LC1188" class="line" lang="plaintext">.BI \-\-fastx_getseq \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1069
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<td class="diff-line-num new_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1189
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1189" class="line" lang="plaintext">Extract sequences from the given FASTA or FASTQ file. Specify a label</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1070
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<td class="diff-line-num new_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1190
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1190" class="line" lang="plaintext">to match using the \-\-label option. Output files are specified with</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1071
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<td class="diff-line-num new_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1191
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1191" class="line" lang="plaintext">the \-\-fastaout, \-\-fastqout, \-\-notmatched and \-\-notmatchedfq</span>
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<td class="diff-line-num old_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1072
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<td class="diff-line-num new_line" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1192
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<pre style="margin: 0;"> <span id="LC1192" class="line" lang="plaintext">options.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); 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="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1193
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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="plaintext">.TAG fastx_getseqs</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1073
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<td class="diff-line-num new_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1194
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<pre style="margin: 0;"> <span id="LC1194" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1074
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<td class="diff-line-num new_line" data-linenumber="1195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1195
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<pre style="margin: 0;"> <span id="LC1195" class="line" lang="plaintext">.BI \-\-fastx_getseqs \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1075
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<td class="diff-line-num new_line" data-linenumber="1196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1196
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1196" class="line" lang="plaintext">Extract sequences from the given FASTA or FASTQ file. Specify the</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1077" style="width: 35px; color: rgba(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="1198" style="width: 35px; color: rgba(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">@@ -1077,6 +1198,7 @@ label or labels to match using one of the following options: \-\-label,</td>
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<td class="diff-line-num old_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1077
</td>
<td class="diff-line-num new_line" data-linenumber="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1198
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<pre style="margin: 0;"> <span id="LC1198" class="line" lang="plaintext">\-\-labels, \-\-label_word, or \-\-label_words. Output</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="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1078
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<td class="diff-line-num new_line" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1199
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<pre style="margin: 0;"> <span id="LC1199" class="line" lang="plaintext">files are specified with the \-\-fastaout, \-\-fastqout,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1079
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<td class="diff-line-num new_line" data-linenumber="1200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1200
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1200" class="line" lang="plaintext">\-\-notmatched and \-\-notmatchedfq options.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1201
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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="plaintext">.TAG fastx_getsubseq</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1080
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<td class="diff-line-num new_line" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1202
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1202" class="line" lang="plaintext">.TP</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="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1081
</td>
<td class="diff-line-num new_line" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1203
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1203" class="line" lang="plaintext">.BI \-\-fastx_getsubseq \0filename</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="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1082
</td>
<td class="diff-line-num new_line" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1204
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1204" class="line" lang="plaintext">Extract a certain part of some of the sequences in the given FASTA or</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1085" style="width: 35px; color: rgba(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="1207" style="width: 35px; color: rgba(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">@@ -1085,11 +1207,13 @@ option. Specify the subsequence range to be extracted with the</td>
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<td class="diff-line-num old_line" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1085
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<td class="diff-line-num new_line" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1207
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1207" class="line" lang="plaintext">\-\-subseq_start and \-\-subseq_end options. Output files are</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="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">
1086
</td>
<td class="diff-line-num new_line" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1208
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1208" class="line" lang="plaintext">specified with the \-\-fastaout, \-\-fastqout, \-\-notmatched and</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="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1087
</td>
<td class="diff-line-num new_line" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1209
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1209" class="line" lang="plaintext">\-\-notmatchedfq options.</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="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="plaintext">.TAG label</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1088
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<td class="diff-line-num new_line" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1211
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1211" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1089
</td>
<td class="diff-line-num new_line" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1212
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1212" class="line" lang="plaintext">.BI \-\-label \0string</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1090
</td>
<td class="diff-line-num new_line" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1213
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1213" class="line" lang="plaintext">Specifiy the label to match in the sequence header. Unless the</span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="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">
1091
</td>
<td class="diff-line-num new_line" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1214
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1214" class="line" lang="plaintext">\-\-label_substr_match option is given, the label must match the</span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="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">
1092
</td>
<td class="diff-line-num new_line" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1215
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1215" class="line" lang="plaintext">entire header. The comparison is not case-sensitive.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1216
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="plaintext">.TAG label_field</span>
</pre>
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</tr>
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<td class="diff-line-num old_line" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1093
</td>
<td class="diff-line-num new_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1217
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1217" class="line" lang="plaintext">.TP</span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1094
</td>
<td class="diff-line-num new_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1218
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1218" class="line" lang="plaintext">.BI \-\-label_field \0string</span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1095
</td>
<td class="diff-line-num new_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1219
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1219" class="line" lang="plaintext">Specify a field name to be used when matching using the \-\-label_word</span>
</pre>
</td>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1098" style="width: 35px; color: rgba(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="1222" style="width: 35px; color: rgba(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">@@ -1098,17 +1222,20 @@ must precede the word to be matched with an equals sign (=) in</td>
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<td class="diff-line-num old_line" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1098
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<td class="diff-line-num new_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1222
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1222" class="line" lang="plaintext">between. The field must be delimited by semicolons or the beginning or</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1099
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<td class="diff-line-num new_line" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1223
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1223" class="line" lang="plaintext">end of the header. The following header will match the label 123 in</span>
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<td class="diff-line-num old_line" data-linenumber="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1100
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<td class="diff-line-num new_line" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1224
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1224" class="line" lang="plaintext">the field abc: "seq1;abc=123".</span>
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<td class="diff-line-num new old_line" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1225
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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="plaintext">.TAG label_substr_match</span>
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<td class="diff-line-num old_line" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1101
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<td class="diff-line-num new_line" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1226
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1226" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1102
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<td class="diff-line-num new_line" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1227
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1227" class="line" lang="plaintext">.BI \-\-label_substr_match</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1103
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<td class="diff-line-num new_line" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1228
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1228" class="line" lang="plaintext">The labels specified with the \-\-label or the \-\-labels option may</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="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1104
</td>
<td class="diff-line-num new_line" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1229
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1229" class="line" lang="plaintext">match anywhere in the header if this option is given. Otherwise a</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1105
</td>
<td class="diff-line-num new_line" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1230
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1230" class="line" lang="plaintext">label needs to match the entire header.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1231
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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="plaintext">.TAG label_word</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1106
</td>
<td class="diff-line-num new_line" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1232
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1232" class="line" lang="plaintext">.TP</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="1107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1107
</td>
<td class="diff-line-num new_line" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1233
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1233" class="line" lang="plaintext">.BI \-\-label_word \0string</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="1108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1108
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<td class="diff-line-num new_line" data-linenumber="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1234
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1234" class="line" lang="plaintext">Specifiy a word to match in the sequence header. Words are defined as</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="1109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1109
</td>
<td class="diff-line-num new_line" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1235
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1235" class="line" lang="plaintext">strings delimited by either the start or end of the header or by any</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="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1110
</td>
<td class="diff-line-num new_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1236
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1236" class="line" lang="plaintext">symbol that is not a letter (A-Z, a-z) or digit (0-9). The comparison is</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="1111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1111
</td>
<td class="diff-line-num new_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">
1237
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1237" class="line" lang="plaintext">case-sensitive.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="plaintext">.TAG label_words</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1112
</td>
<td class="diff-line-num new_line" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1239
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1239" class="line" lang="plaintext">.TP</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="1113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1113
</td>
<td class="diff-line-num new_line" data-linenumber="1240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1240
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1240" class="line" lang="plaintext">.BI \-\-label_words \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1114
</td>
<td class="diff-line-num new_line" data-linenumber="1241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1241
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1241" class="line" lang="plaintext">Specify a file containing words to be matched against the sequence</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1116" style="width: 35px; color: rgba(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="1243" style="width: 35px; color: rgba(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">@@ -1116,27 +1243,32 @@ headers. The plain text file must contain one word on each line.</td>
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<td class="diff-line-num old_line" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1116
</td>
<td class="diff-line-num new_line" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1243
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1243" class="line" lang="plaintext">Words are defined as strings delimited by either the start or end of</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="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1117
</td>
<td class="diff-line-num new_line" data-linenumber="1244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1244
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1244" class="line" lang="plaintext">the header or by any symbol that is not a letter (A-Z, a-z) or digit</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1118
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<td class="diff-line-num new_line" data-linenumber="1245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1245
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1245" class="line" lang="plaintext">(0-9). The comparison is case-sensitive.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="plaintext">.TAG labels</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1119
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<td class="diff-line-num new_line" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1247
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<pre style="margin: 0;"> <span id="LC1247" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1120
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<td class="diff-line-num new_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1248
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<pre style="margin: 0;"> <span id="LC1248" class="line" lang="plaintext">.BI \-\-labels \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1121
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<td class="diff-line-num new_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1249
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<pre style="margin: 0;"> <span id="LC1249" class="line" lang="plaintext">Specify a file containing labels to be matched against the sequence</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1122
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<td class="diff-line-num new_line" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1250
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<pre style="margin: 0;"> <span id="LC1250" class="line" lang="plaintext">headers. The plain text file must contain one label on each</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1123
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<td class="diff-line-num new_line" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1251
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<pre style="margin: 0;"> <span id="LC1251" class="line" lang="plaintext">line. Unless the \-\-label_substr_match option is given, a label must</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1124
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<td class="diff-line-num new_line" data-linenumber="1252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1252
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<pre style="margin: 0;"> <span id="LC1252" class="line" lang="plaintext">match the entire header. The comparison is not case-sensitive.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1253
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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="plaintext">.TAG notmatched</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1125
</td>
<td class="diff-line-num new_line" data-linenumber="1254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1254
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1254" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1126
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<td class="diff-line-num new_line" data-linenumber="1255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1255
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<pre style="margin: 0;"> <span id="LC1255" class="line" lang="plaintext">.BI \-\-notmatched \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1127
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<td class="diff-line-num new_line" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1256
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1256" class="line" lang="plaintext">Write the sequences that were not extracted to the file with the given</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1128
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<td class="diff-line-num new_line" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1257
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1257" class="line" lang="plaintext">name, in FASTA format.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="plaintext">.TAG notmatchedfq</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1129
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<td class="diff-line-num new_line" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1259
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1259" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1130
</td>
<td class="diff-line-num new_line" data-linenumber="1260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1260
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1260" class="line" lang="plaintext">.BI \-\-notmatchedfq \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1131
</td>
<td class="diff-line-num new_line" data-linenumber="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1261
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1261" class="line" lang="plaintext">Write the sequences that were not extracted to the file with the given</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1132
</td>
<td class="diff-line-num new_line" data-linenumber="1262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1262
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1262" class="line" lang="plaintext">name, in FASTQ format. This option is illegal if the input is in FASTA</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1133
</td>
<td class="diff-line-num new_line" data-linenumber="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1263
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1263" class="line" lang="plaintext">format.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1264
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<pre style="margin: 0;">+<span id="LC1264" class="line" lang="plaintext">.TAG subseq_end</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1134
</td>
<td class="diff-line-num new_line" data-linenumber="1265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1265
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1265" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1135
</td>
<td class="diff-line-num new_line" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1266
</td>
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<pre style="margin: 0;"> <span id="LC1266" class="line" lang="plaintext">.BI \-\-subseq_end\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1136
</td>
<td class="diff-line-num new_line" data-linenumber="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1267
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1267" class="line" lang="plaintext">Specifiy the end position in the sequences when extracting</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="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1137
</td>
<td class="diff-line-num new_line" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1268
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1268" class="line" lang="plaintext">subsequences using the \-\-fastx_getsubseq command. Positions are</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="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1138
</td>
<td class="diff-line-num new_line" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1269
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1269" class="line" lang="plaintext">1-based, so the sequences start at position 1. The default is to end</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1139
</td>
<td class="diff-line-num new_line" data-linenumber="1270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1270
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1270" class="line" lang="plaintext">at the end of the sequence if this option is not specified.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="plaintext">.TAG subseq_start</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1140
</td>
<td class="diff-line-num new_line" data-linenumber="1272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1272
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1272" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1141
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1273
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<pre style="margin: 0;"> <span id="LC1273" class="line" lang="plaintext">.BI \-\-subseq_start\~ "positive integer"</span>
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<td class="diff-line-num 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">
1142
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1274
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<pre style="margin: 0;"> <span id="LC1274" class="line" lang="plaintext">Specifiy the starting position in the sequences when extracting</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1147" style="width: 35px; color: rgba(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="1279" style="width: 35px; color: rgba(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">@@ -1147,6 +1279,7 @@ specified.</td>
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1147
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<td class="diff-line-num new_line" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1279
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="plaintext">.RE</span>
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<td class="diff-line-num old_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1148
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1280
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<pre style="margin: 0;"> <span id="LC1280" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num old_line" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1149
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1281
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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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<td class="diff-line-num new old_line" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); 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="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="plaintext">.TAG fasta-fastq-file-processing-options</span>
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1150
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1283
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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="plaintext">FASTA/FASTQ file processing options:</span>
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<td class="diff-line-num old_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1151
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<td class="diff-line-num new_line" data-linenumber="1284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1284
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<pre style="margin: 0;"> <span id="LC1284" class="line" lang="plaintext">.RS</span>
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<td class="diff-line-num old_line" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1152
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<td class="diff-line-num new_line" data-linenumber="1285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1285
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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1164" style="width: 35px; color: rgba(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="1297" style="width: 35px; color: rgba(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">@@ -1164,6 +1297,7 @@ merged using the \-\-fastq_mergepairs command. The \-\-fastx_revcomp</td>
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1164
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1297
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<pre style="margin: 0;"> <span id="LC1297" class="line" lang="plaintext">command reverse-complements sequences. Finally, the \-\-sff_convert</span>
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<td class="diff-line-num old_line" data-linenumber="1165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1165
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1298
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<pre style="margin: 0;"> <span id="LC1298" class="line" lang="plaintext">command can be used to convert SFF files to FASTQ.</span>
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<td class="diff-line-num old_line" data-linenumber="1166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1166
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1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="plaintext">.PP</span>
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1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="plaintext">.TAG eeout</span>
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1167
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1301
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<pre style="margin: 0;"> <span id="LC1301" class="line" lang="plaintext">.TP 9</span>
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<td class="diff-line-num old_line" data-linenumber="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1168
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1302
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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="plaintext">.B \-\-eeout</span>
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<td class="diff-line-num old_line" data-linenumber="1169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1169
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1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="plaintext">When using \-\-fastq_filter or \-\-fastq_mergepairs, include the</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1171" style="width: 35px; color: rgba(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="1305" style="width: 35px; color: rgba(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">@@ -1171,6 +1305,7 @@ number of expected errors (ee) in the sequence header of FASTQ and</td>
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<td class="diff-line-num old_line" data-linenumber="1171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1171
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1305
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<pre style="margin: 0;"> <span id="LC1305" class="line" lang="plaintext">FASTA files. This option is a synonym of the \-\-fastq_eeout</span>
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<td class="diff-line-num old_line" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1172
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1306
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<pre style="margin: 0;"> <span id="LC1306" class="line" lang="plaintext">option. Use the \-\-xee option to remove this information from</span>
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1173
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1307
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="plaintext">headers.</span>
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<td class="diff-line-num new new_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="plaintext">.TAG eetabbedout</span>
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1174
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1309
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<pre style="margin: 0;"> <span id="LC1309" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1175
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<td class="diff-line-num new_line" data-linenumber="1310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1310
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<pre style="margin: 0;"> <span id="LC1310" class="line" lang="plaintext">.BI \-\-eetabbedout \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1176
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<td class="diff-line-num new_line" data-linenumber="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1311
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<pre style="margin: 0;"> <span id="LC1311" class="line" lang="plaintext">When specified with the \-\-fastq_mergepairs command, write statistics</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1181" style="width: 35px; color: rgba(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">@@ -1181,33 +1316,40 @@ reverse read, the number of observed errors in the forward read, and</td>
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1181
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1316
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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="plaintext">the number of observed errors in the reverse read. The observed number</span>
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<td class="diff-line-num old_line" data-linenumber="1182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1182
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<td class="diff-line-num new_line" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1317
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<pre style="margin: 0;"> <span id="LC1317" class="line" lang="plaintext">of errors are the number of differences in the overlap region of the</span>
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<td class="diff-line-num old_line" data-linenumber="1183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1183
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<td class="diff-line-num new_line" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1318
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<pre style="margin: 0;"> <span id="LC1318" class="line" lang="plaintext">merged sequence relative to each of the reads in the pair.</span>
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<td class="diff-line-num new old_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); 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="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="plaintext">.TAG fastaout</span>
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<td class="diff-line-num old_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1184
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<td class="diff-line-num new_line" data-linenumber="1320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1320
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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="1185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1185
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<td class="diff-line-num new_line" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1321
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="plaintext">.BI \-\-fastaout \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1186
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<td class="diff-line-num new_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1322
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<pre style="margin: 0;"> <span id="LC1322" class="line" lang="plaintext">When using \-\-fastq_filter, \-\-fastq_mergepairs or \-\-fastx_filter,</span>
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<td class="diff-line-num old_line" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1187
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<td class="diff-line-num new_line" data-linenumber="1323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1323
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<pre style="margin: 0;"> <span id="LC1323" class="line" lang="plaintext">write to the given FASTA-formatted file the sequences passing the</span>
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<td class="diff-line-num old_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1188
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<td class="diff-line-num new_line" data-linenumber="1324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1324
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="plaintext">filter, or the merged sequences.</span>
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<td class="diff-line-num new old_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); 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="1325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1325
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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="plaintext">.TAG fastaout_rev</span>
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<td class="diff-line-num old_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1189
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<td class="diff-line-num new_line" data-linenumber="1326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1326
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<pre style="margin: 0;"> <span id="LC1326" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1190
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<td class="diff-line-num new_line" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1327
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<pre style="margin: 0;"> <span id="LC1327" class="line" lang="plaintext">.BI \-\-fastaout_rev \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1191
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<td class="diff-line-num new_line" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1328
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<pre style="margin: 0;"> <span id="LC1328" class="line" lang="plaintext">When using \-\-fastq_filter, or \-\-fastx_filter,</span>
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<td class="diff-line-num old_line" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1192
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<td class="diff-line-num new_line" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1329
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<pre style="margin: 0;"> <span id="LC1329" class="line" lang="plaintext">write to the given FASTA-formatted file the reverse reads passing the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1193
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<td class="diff-line-num new_line" data-linenumber="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1330
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<pre style="margin: 0;"> <span id="LC1330" class="line" lang="plaintext">filter.</span>
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<td class="diff-line-num new old_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); 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="1331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="plaintext">.TAG fastaout_notmerged_fwd</span>
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<td class="diff-line-num old_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1194
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<td class="diff-line-num new_line" data-linenumber="1332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1332
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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1195
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<td class="diff-line-num new_line" data-linenumber="1333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1333
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<pre style="margin: 0;"> <span id="LC1333" class="line" lang="plaintext">.BI \-\-fastaout_notmerged_fwd \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1196
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<td class="diff-line-num new_line" data-linenumber="1334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1334
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<pre style="margin: 0;"> <span id="LC1334" class="line" lang="plaintext">When using \-\-fastq_mergepairs, write forward reads not merged to the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1197
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<td class="diff-line-num new_line" data-linenumber="1335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1335
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<pre style="margin: 0;"> <span id="LC1335" class="line" lang="plaintext">specified FASTA file.</span>
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<td class="diff-line-num new old_line" data-linenumber="1198" style="width: 35px; color: rgba(0,0,0,0.3); 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="1336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="plaintext">.TAG fastaout_notmerged_rev</span>
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<td class="diff-line-num old_line" data-linenumber="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1198
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<td class="diff-line-num new_line" data-linenumber="1337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1337
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<pre style="margin: 0;"> <span id="LC1337" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1199
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<td class="diff-line-num new_line" data-linenumber="1338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1338
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<pre style="margin: 0;"> <span id="LC1338" class="line" lang="plaintext">.BI \-\-fastaout_notmerged_rev \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1200
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<td class="diff-line-num new_line" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1339
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<pre style="margin: 0;"> <span id="LC1339" class="line" lang="plaintext">When using \-\-fastq_mergepairs, write reverse reads not merged to the</span>
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<td class="diff-line-num old_line" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1201
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<td class="diff-line-num new_line" data-linenumber="1340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1340
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<pre style="margin: 0;"> <span id="LC1340" class="line" lang="plaintext">specified FASTA file.</span>
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<td class="diff-line-num new old_line" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); 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="1341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="plaintext">.TAG fastaout_discarded</span>
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<td class="diff-line-num old_line" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1202
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<td class="diff-line-num new_line" data-linenumber="1342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1342
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1203
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<td class="diff-line-num new_line" data-linenumber="1343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1343
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="plaintext">.BI \-\-fastaout_discarded \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1204
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<td class="diff-line-num new_line" data-linenumber="1344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1344
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="plaintext">Write sequences that do not pass the filter of the \-\-fastq_filter or</span>
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<td class="diff-line-num old_line" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1205
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<td class="diff-line-num new_line" data-linenumber="1345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1345
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<pre style="margin: 0;"> <span id="LC1345" class="line" lang="plaintext">\-\-fastx_filter command to the given FASTA-formatted file.</span>
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<td class="diff-line-num new old_line" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); 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="1346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1346
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="plaintext">.TAG fastaout_discarded_rev</span>
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<td class="diff-line-num old_line" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1206
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<td class="diff-line-num new_line" data-linenumber="1347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1347
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<pre style="margin: 0;"> <span id="LC1347" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1207
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<td class="diff-line-num new_line" data-linenumber="1348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1348
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<pre style="margin: 0;"> <span id="LC1348" class="line" lang="plaintext">.BI \-\-fastaout_discarded_rev \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1208
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<td class="diff-line-num new_line" data-linenumber="1349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1349
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<pre style="margin: 0;"> <span id="LC1349" class="line" lang="plaintext">Write reverse reads that do not pass the filter of the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1209
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<td class="diff-line-num new_line" data-linenumber="1350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1350
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<pre style="margin: 0;"> <span id="LC1350" class="line" lang="plaintext">\-\-fastq_filter or \-\-fastx_filter command to the given</span>
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<td class="diff-line-num old_line" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1210
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<td class="diff-line-num new_line" data-linenumber="1351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1351
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<pre style="margin: 0;"> <span id="LC1351" class="line" lang="plaintext">FASTA-formatted file.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); 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="1352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1352
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<pre style="margin: 0;">+<span id="LC1352" class="line" lang="plaintext">.TAG fastq_allowmergestagger</span>
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<td class="diff-line-num old_line" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1211
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<td class="diff-line-num new_line" data-linenumber="1353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1353
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<pre style="margin: 0;"> <span id="LC1353" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1212
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<td class="diff-line-num new_line" data-linenumber="1354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1354
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<pre style="margin: 0;"> <span id="LC1354" class="line" lang="plaintext">.B \-\-fastq_allowmergestagger</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1213
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<td class="diff-line-num new_line" data-linenumber="1355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1355
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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="plaintext">When using \-\-fastq_mergepairs, allow to merge staggered read</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1217" style="width: 35px; color: rgba(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="1359" style="width: 35px; color: rgba(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">@@ -1217,6 +1359,7 @@ situation can occur when a very short fragment is sequenced. The 3'</td>
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<td class="diff-line-num old_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1217
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<td class="diff-line-num new_line" data-linenumber="1359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1359
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<pre style="margin: 0;"> <span id="LC1359" class="line" lang="plaintext">overhang of the reverse read is not included in the merged</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1218
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<td class="diff-line-num new_line" data-linenumber="1360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1360
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1360" class="line" lang="plaintext">sequence. The opposite option is the \-\-fastq_nostagger option. The</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1219
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<td class="diff-line-num new_line" data-linenumber="1361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1361
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1361" class="line" lang="plaintext">default is to discard staggered pairs.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); 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="1362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1362
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<pre style="margin: 0;">+<span id="LC1362" class="line" lang="plaintext">.TAG fastq_ascii</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1220
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<td class="diff-line-num new_line" data-linenumber="1363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1363
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1363" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1221
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<td class="diff-line-num new_line" data-linenumber="1364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1364
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<pre style="margin: 0;"> <span id="LC1364" class="line" lang="plaintext">.BI \-\-fastq_ascii\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1222
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<td class="diff-line-num new_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1365
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1365" class="line" lang="plaintext">Define the ASCII character number used as the basis for the FASTQ</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1224" style="width: 35px; color: rgba(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="1367" style="width: 35px; color: rgba(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">@@ -1224,12 +1367,14 @@ quality score. The default is 33, which is used by the Sanger /</td>
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<td class="diff-line-num old_line" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1224
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<td class="diff-line-num new_line" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1367
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1367" class="line" lang="plaintext">Illumina 1.8+ FASTQ format (phred+33). The value 64 is used by the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1225
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<td class="diff-line-num new_line" data-linenumber="1368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1368
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1368" class="line" lang="plaintext">Solexa, Illumina 1.3+ and Illumina 1.5+ formats (phred+64). Only 33</span>
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<td class="diff-line-num old_line" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1226
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<td class="diff-line-num new_line" data-linenumber="1369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1369
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<pre style="margin: 0;"> <span id="LC1369" class="line" lang="plaintext">and 64 are valid arguments.</span>
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<td class="diff-line-num new old_line" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); 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="1370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1370
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<pre style="margin: 0;">+<span id="LC1370" class="line" lang="plaintext">.TAG fastq_asciiout</span>
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<td class="diff-line-num old_line" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1227
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<td class="diff-line-num new_line" data-linenumber="1371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1371
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<pre style="margin: 0;"> <span id="LC1371" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1228
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<td class="diff-line-num new_line" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1372
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<pre style="margin: 0;"> <span id="LC1372" class="line" lang="plaintext">.BI \-\-fastq_asciiout\~ "positive integer"</span>
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<td class="diff-line-num old_line" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1229
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<td class="diff-line-num new_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1373
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<pre style="margin: 0;"> <span id="LC1373" class="line" lang="plaintext">When using \-\-fastq_convert or \-\-sff_convert, define the ASCII</span>
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<td class="diff-line-num old_line" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1230
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<td class="diff-line-num new_line" data-linenumber="1374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1374
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<pre style="margin: 0;"> <span id="LC1374" class="line" lang="plaintext">character number used as the basis for the FASTQ quality score when</span>
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<td class="diff-line-num old_line" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1231
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<td class="diff-line-num new_line" data-linenumber="1375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1375
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<pre style="margin: 0;"> <span id="LC1375" class="line" lang="plaintext">writing FASTQ output files. The default is 33. Only 33 and 64 are</span>
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<td class="diff-line-num old_line" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1232
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<td class="diff-line-num new_line" data-linenumber="1376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1376
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<pre style="margin: 0;"> <span id="LC1376" class="line" lang="plaintext">valid arguments.</span>
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<td class="diff-line-num new old_line" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); 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="1377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1377
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<pre style="margin: 0;">+<span id="LC1377" class="line" lang="plaintext">.TAG fastq_chars</span>
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<td class="diff-line-num old_line" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1233
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<td class="diff-line-num new_line" data-linenumber="1378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1378
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<pre style="margin: 0;"> <span id="LC1378" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1234
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<td class="diff-line-num new_line" data-linenumber="1379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1379
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<pre style="margin: 0;"> <span id="LC1379" class="line" lang="plaintext">.BI \-\-fastq_chars \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1235
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<td class="diff-line-num new_line" data-linenumber="1380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1380
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<pre style="margin: 0;"> <span id="LC1380" class="line" lang="plaintext">Summarize the composition of sequence and quality strings contained in</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1247" style="width: 35px; color: rgba(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="1392" style="width: 35px; color: rgba(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">@@ -1247,6 +1392,7 @@ analyzing the range of observed quality score values. In case of</td>
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<td class="diff-line-num old_line" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1247
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<td class="diff-line-num new_line" data-linenumber="1392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1392
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<pre style="margin: 0;"> <span id="LC1392" class="line" lang="plaintext">success, \-\-fastq_chars suggests values for the \-\-fastq_ascii (33</span>
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<td class="diff-line-num old_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1248
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<td class="diff-line-num new_line" data-linenumber="1393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1393
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<pre style="margin: 0;"> <span id="LC1393" class="line" lang="plaintext">or 64), \-\-fastq_qmin and \-\-fastq_qmax options to be used with the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1249
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<td class="diff-line-num new_line" data-linenumber="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1394
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<pre style="margin: 0;"> <span id="LC1394" class="line" lang="plaintext">other commands that require a FASTQ input file.</span>
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<td class="diff-line-num new old_line" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); 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="1395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1395
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<pre style="margin: 0;">+<span id="LC1395" class="line" lang="plaintext">.TAG fastq_convert</span>
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<td class="diff-line-num old_line" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1250
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<td class="diff-line-num new_line" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1396
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<pre style="margin: 0;"> <span id="LC1396" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1251
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<td class="diff-line-num new_line" data-linenumber="1397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1397
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<pre style="margin: 0;"> <span id="LC1397" class="line" lang="plaintext">.BI \-\-fastq_convert \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1252
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<td class="diff-line-num new_line" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1398
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<pre style="margin: 0;"> <span id="LC1398" class="line" lang="plaintext">Convert between the different variants of the FASTQ file format. The</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1256" style="width: 35px; color: rgba(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="1402" style="width: 35px; color: rgba(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">@@ -1256,6 +1402,7 @@ output quality encoding must be specified with the \-\-fastq_asciiout</td>
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<td class="diff-line-num old_line" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1256
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<td class="diff-line-num new_line" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1402
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<pre style="margin: 0;"> <span id="LC1402" class="line" lang="plaintext">option (default 33). The minimum and maximum output quality scores may</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1257
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<td class="diff-line-num new_line" data-linenumber="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1403
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<pre style="margin: 0;"> <span id="LC1403" class="line" lang="plaintext">be limited using the \-\-fastq_qminout and \-\-fastq_qmaxout</span>
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<td class="diff-line-num old_line" data-linenumber="1258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1258
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<td class="diff-line-num new_line" data-linenumber="1404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1404
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<pre style="margin: 0;"> <span id="LC1404" class="line" lang="plaintext">options. The output file is specified with the \-\-fastqout option.</span>
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<td class="diff-line-num new old_line" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); 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="1405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="plaintext">.TAG fastq_eeout</span>
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<td class="diff-line-num old_line" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1259
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<td class="diff-line-num new_line" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1406
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<pre style="margin: 0;"> <span id="LC1406" class="line" lang="plaintext">.TP</span>
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1260
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1407
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<pre style="margin: 0;"> <span id="LC1407" class="line" lang="plaintext">.B \-\-fastq_eeout</span>
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1261
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1408
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<pre style="margin: 0;"> <span id="LC1408" class="line" lang="plaintext">When using \-\-fastq_filter, \-\-fastx_filter or \-\-fastq_mergepairs,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1263" style="width: 35px; color: rgba(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="1410" style="width: 35px; color: rgba(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">@@ -1263,6 +1410,7 @@ include the number of expected errors (ee) in the sequence header of</td>
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1263
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1410
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<pre style="margin: 0;"> <span id="LC1410" class="line" lang="plaintext">FASTQ and FASTA files. This option is a synonym of the \-\-eeout</span>
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<td class="diff-line-num old_line" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1264
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<td class="diff-line-num new_line" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1411
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<pre style="margin: 0;"> <span id="LC1411" class="line" lang="plaintext">option. Use the \-\-xee option to remove this information from</span>
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<td class="diff-line-num old_line" data-linenumber="1265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1265
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<td class="diff-line-num new_line" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1412
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<pre style="margin: 0;"> <span id="LC1412" class="line" lang="plaintext">headers.</span>
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<td class="diff-line-num new old_line" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); 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="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1413
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="plaintext">.TAG fastq_eestats</span>
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<td class="diff-line-num old_line" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1266
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<td class="diff-line-num new_line" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1267
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<td class="diff-line-num new_line" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1415
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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="plaintext">.BI \-\-fastq_eestats \0filename</span>
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1268
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<td class="diff-line-num new_line" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1416
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<pre style="margin: 0;"> <span id="LC1416" class="line" lang="plaintext">Analyze a FASTQ file and report statistics on the distributions of</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1281,6 +1429,7 @@ EE distributions, the following statistics are included: minimum value</td>
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<td class="diff-line-num old_line" data-linenumber="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1281
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<td class="diff-line-num new_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1429
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<pre style="margin: 0;"> <span id="LC1429" class="line" lang="plaintext">(Hi), and maximum value (Max). The quality encoding and the range of</span>
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<td class="diff-line-num old_line" data-linenumber="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1282
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<td class="diff-line-num new_line" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1430
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<pre style="margin: 0;"> <span id="LC1430" class="line" lang="plaintext">quality values may be specified with \-\-fastq_ascii \-\-fastq_qmin</span>
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<td class="diff-line-num old_line" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1283
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<td class="diff-line-num new_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1431
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<pre style="margin: 0;"> <span id="LC1431" class="line" lang="plaintext">and \-\-fastq_qmax.</span>
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1432
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<pre style="margin: 0;">+<span id="LC1432" class="line" lang="plaintext">.TAG fastq_eestats2</span>
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1284
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1433
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<pre style="margin: 0;"> <span id="LC1433" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="1285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1285
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1434
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<pre style="margin: 0;"> <span id="LC1434" class="line" lang="plaintext">.BI \-\-fastq_eestats2 \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1286
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<td class="diff-line-num new_line" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1435
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<pre style="margin: 0;"> <span id="LC1435" class="line" lang="plaintext">Analyze the specified FASTQ file and report statistics on the number</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1305" style="width: 35px; color: rgba(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="1454" style="width: 35px; color: rgba(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">@@ -1305,11 +1454,13 @@ expected error (EE) cutoffs may be specified with the \-\-ee_cutoffs</td>
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<td class="diff-line-num old_line" data-linenumber="1305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1305
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1454
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<pre style="margin: 0;"> <span id="LC1454" class="line" lang="plaintext">option which requires a comma-separated list of floating point numbers</span>
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<td class="diff-line-num old_line" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1306
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<td class="diff-line-num new_line" data-linenumber="1455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1455
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<pre style="margin: 0;"> <span id="LC1455" class="line" lang="plaintext">as its argument. The default setting is "0.5,1.0,2.0" that indicates</span>
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<td class="diff-line-num old_line" data-linenumber="1307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1307
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<td class="diff-line-num new_line" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1456
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<pre style="margin: 0;"> <span id="LC1456" class="line" lang="plaintext">that expected error levels of 0.5, 1.0 and 2.0 should be used.</span>
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<td class="diff-line-num new old_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1457
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<pre style="margin: 0;">+<span id="LC1457" class="line" lang="plaintext">.TAG fastq_filter</span>
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<td class="diff-line-num old_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1308
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<td class="diff-line-num new_line" data-linenumber="1458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1458
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<pre style="margin: 0;"> <span id="LC1458" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1309
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<td class="diff-line-num new_line" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1459
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<pre style="margin: 0;"> <span id="LC1459" class="line" lang="plaintext">.BI \-\-fastq_filter \0filename</span>
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1310
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<td class="diff-line-num new_line" data-linenumber="1460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1460
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<pre style="margin: 0;"> <span id="LC1460" class="line" lang="plaintext">Trim and/or filter sequences in the given FASTQ file. Similar to</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1311
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<td class="diff-line-num new_line" data-linenumber="1461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1461
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<pre style="margin: 0;"> <span id="LC1461" class="line" lang="plaintext">the \-\-fastx_filter command, but works only on FASTQ files. See</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1312
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<td class="diff-line-num new_line" data-linenumber="1462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1462
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<pre style="margin: 0;"> <span id="LC1462" class="line" lang="plaintext">\-\-fastx_filter for details.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); 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="1463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1463
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<pre style="margin: 0;">+<span id="LC1463" class="line" lang="plaintext">.TAG fastq_join</span>
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<td class="diff-line-num old_line" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1313
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<td class="diff-line-num new_line" data-linenumber="1464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1464
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<pre style="margin: 0;"> <span id="LC1464" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1314
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<td class="diff-line-num new_line" data-linenumber="1465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1465
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<pre style="margin: 0;"> <span id="LC1465" class="line" lang="plaintext">.BI \-\-fastq_join\0 filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1315
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<td class="diff-line-num new_line" data-linenumber="1466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1466
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1466" class="line" lang="plaintext">Join paired-end sequence reads into one sequence and add a gap between</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1326" style="width: 35px; color: rgba(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="1477" style="width: 35px; color: rgba(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">@@ -1326,12 +1477,14 @@ IIIIIIII, corresponding to a base quality score of 40 (a very high</td>
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<td class="diff-line-num old_line" data-linenumber="1326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1326
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<td class="diff-line-num new_line" data-linenumber="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1477
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<pre style="margin: 0;"> <span id="LC1477" class="line" lang="plaintext">quality score with error probability 0.0001). The joined sequences are</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1327
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<td class="diff-line-num new_line" data-linenumber="1478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1478
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<pre style="margin: 0;"> <span id="LC1478" class="line" lang="plaintext">output to the file(s) specified with the \-\-fastaout or \-\-fastqout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1328
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<td class="diff-line-num new_line" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1479
</td>
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<pre style="margin: 0;"> <span id="LC1479" class="line" lang="plaintext">options.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1480
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<pre style="margin: 0;">+<span id="LC1480" class="line" lang="plaintext">.TAG fastq_maxdiffs</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1329
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<td class="diff-line-num new_line" data-linenumber="1481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1481
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1481" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1330
</td>
<td class="diff-line-num new_line" data-linenumber="1482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1482
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<pre style="margin: 0;"> <span id="LC1482" class="line" lang="plaintext">.BI \-\-fastq_maxdiffs\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1331
</td>
<td class="diff-line-num new_line" data-linenumber="1483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1483
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1483" class="line" lang="plaintext">When using \-\-fastq_mergepairs, specify the maximum number of</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="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">
1332
</td>
<td class="diff-line-num new_line" data-linenumber="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1484
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1484" class="line" lang="plaintext">non-matching nucleotides allowed in the overlap region. That option</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1333
</td>
<td class="diff-line-num new_line" data-linenumber="1485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1485
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1485" class="line" lang="plaintext">has a strong influence on the merging success rate. The default</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1334
</td>
<td class="diff-line-num new_line" data-linenumber="1486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1486
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<pre style="margin: 0;"> <span id="LC1486" class="line" lang="plaintext">value is 10.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1487
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<pre style="margin: 0;">+<span id="LC1487" class="line" lang="plaintext">.TAG fastq_maxdiffpct</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1335
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<td class="diff-line-num new_line" data-linenumber="1488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1488
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<pre style="margin: 0;"> <span id="LC1488" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1336
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<td class="diff-line-num new_line" data-linenumber="1489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1489
</td>
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<pre style="margin: 0;"> <span id="LC1489" class="line" lang="plaintext">.BI \-\-fastq_maxdiffpct\~ real</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1337
</td>
<td class="diff-line-num new_line" data-linenumber="1490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1490
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<pre style="margin: 0;"> <span id="LC1490" class="line" lang="plaintext">When using \-\-fastq_mergepairs, specify the maximum percentage of</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1339" style="width: 35px; color: rgba(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="1492" style="width: 35px; color: rgba(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">@@ -1339,27 +1492,33 @@ non-matching nucleotides allowed in the overlap region. The default</td>
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<td class="diff-line-num old_line" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1339
</td>
<td class="diff-line-num new_line" data-linenumber="1492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1492
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1492" class="line" lang="plaintext">value is 100.0%. There are other more sophisticated rules in the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1340
</td>
<td class="diff-line-num new_line" data-linenumber="1493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1493
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1493" class="line" lang="plaintext">merging algorithm that will discard read pairs with a high fraction of</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1341
</td>
<td class="diff-line-num new_line" data-linenumber="1494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1494
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<pre style="margin: 0;"> <span id="LC1494" class="line" lang="plaintext">mismatches.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1495
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<pre style="margin: 0;">+<span id="LC1495" class="line" lang="plaintext">.TAG fastq_maxee</span>
</pre>
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1342
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<td class="diff-line-num new_line" data-linenumber="1496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1496
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<pre style="margin: 0;"> <span id="LC1496" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1343
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<td class="diff-line-num new_line" data-linenumber="1497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1497
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<pre style="margin: 0;"> <span id="LC1497" class="line" lang="plaintext">.BI \-\-fastq_maxee\~ real</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1344
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<td class="diff-line-num new_line" data-linenumber="1498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1498
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<pre style="margin: 0;"> <span id="LC1498" class="line" lang="plaintext">When using \-\-fastq_filter, \-\-fastq_mergepairs or \-\-fastx_filter,</span>
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<td class="diff-line-num old_line" data-linenumber="1345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1345
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<td class="diff-line-num new_line" data-linenumber="1499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1499
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<pre style="margin: 0;"> <span id="LC1499" class="line" lang="plaintext">discard sequences with more than the specified number of expected</span>
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<td class="diff-line-num old_line" data-linenumber="1346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1346
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<td class="diff-line-num new_line" data-linenumber="1500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1500
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<pre style="margin: 0;"> <span id="LC1500" class="line" lang="plaintext">errors.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1501
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<pre style="margin: 0;">+<span id="LC1501" class="line" lang="plaintext">.TAG fastq_maxee_rate</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1347
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<td class="diff-line-num new_line" data-linenumber="1502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1502
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<pre style="margin: 0;"> <span id="LC1502" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1348
</td>
<td class="diff-line-num new_line" data-linenumber="1503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1503
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<pre style="margin: 0;"> <span id="LC1503" class="line" lang="plaintext">.BI \-\-fastq_maxee_rate\~ real</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1349
</td>
<td class="diff-line-num new_line" data-linenumber="1504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1504
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1504" class="line" lang="plaintext">When using \-\-fastq_filter or \-\-fastx_filter, discard sequences</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="1350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1350
</td>
<td class="diff-line-num new_line" data-linenumber="1505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1505
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1505" class="line" lang="plaintext">with more than the specified number of expected errors per base.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1506
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<pre style="margin: 0;">+<span id="LC1506" class="line" lang="plaintext">.TAG fastq_maxlen</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1351
</td>
<td class="diff-line-num new_line" data-linenumber="1507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1507
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1507" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1352
</td>
<td class="diff-line-num new_line" data-linenumber="1508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1508
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<pre style="margin: 0;"> <span id="LC1508" class="line" lang="plaintext">.BI \-\-fastq_maxlen\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1353
</td>
<td class="diff-line-num new_line" data-linenumber="1509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1509
</td>
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<pre style="margin: 0;"> <span id="LC1509" class="line" lang="plaintext">When using \-\-fastq_filter, \-\-fastq_mergepairs or \-\-fastx_filter,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1354
</td>
<td class="diff-line-num new_line" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1510
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1510" class="line" lang="plaintext">discard sequences with more than the specified number of bases.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1511
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<pre style="margin: 0;">+<span id="LC1511" class="line" lang="plaintext">.TAG fastq_maxmergelen</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1355
</td>
<td class="diff-line-num new_line" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1512
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1512" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1356
</td>
<td class="diff-line-num new_line" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1513
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1513" class="line" lang="plaintext">.BI \-\-fastq_maxmergelen\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1357
</td>
<td class="diff-line-num new_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1514
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1514" class="line" lang="plaintext">When using \-\-fastq_mergepairs, specify the maximum length of the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1358
</td>
<td class="diff-line-num new_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1515
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1515" class="line" lang="plaintext">merged sequence. By default there is no limit.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1516
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<pre style="margin: 0;">+<span id="LC1516" class="line" lang="plaintext">.TAG fastq_maxns</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1359
</td>
<td class="diff-line-num new_line" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1517
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1517" class="line" lang="plaintext">.TP</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="1360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1360
</td>
<td class="diff-line-num new_line" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1518
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1518" class="line" lang="plaintext">.BI \-\-fastq_maxns\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1361
</td>
<td class="diff-line-num new_line" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1519
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1519" class="line" lang="plaintext">When using \-\-fastq_filter, \-\-fastq_mergepairs or \-\-fastx_filter,</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="1362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1362
</td>
<td class="diff-line-num new_line" data-linenumber="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1520
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1520" class="line" lang="plaintext">discard sequences with more than the specified number of N's.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1521
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<pre style="margin: 0;">+<span id="LC1521" class="line" lang="plaintext">.TAG fastq_mergepairs</span>
</pre>
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1363
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1522
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<pre style="margin: 0;"> <span id="LC1522" class="line" lang="plaintext">.TP</span>
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1364
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1523
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<pre style="margin: 0;"> <span id="LC1523" class="line" lang="plaintext">.BI \-\-fastq_mergepairs\0 filename</span>
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1365
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1524
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<pre style="margin: 0;"> <span id="LC1524" class="line" lang="plaintext">Merge paired-end sequence reads into one sequence. The forward reads</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1390" style="width: 35px; color: rgba(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="1549" style="width: 35px; color: rgba(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">@@ -1390,46 +1549,55 @@ may be specified with the \-\-fastq_minmergelen and</td>
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<td class="diff-line-num old_line" data-linenumber="1390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1390
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<td class="diff-line-num new_line" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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<td class="diff-line-num old_line" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1391
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<td class="diff-line-num new_line" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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<td class="diff-line-num old_line" data-linenumber="1392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1392
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<td class="diff-line-num new_line" data-linenumber="1551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1551
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<pre style="margin: 0;"> <span id="LC1551" class="line" lang="plaintext">and \-\-label_suffix.</span>
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<td class="diff-line-num new old_line" data-linenumber="1393" style="width: 35px; color: rgba(0,0,0,0.3); 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="1552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1552
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<pre style="margin: 0;">+<span id="LC1552" class="line" lang="plaintext">.TAG fastq_minlen</span>
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<td class="diff-line-num old_line" data-linenumber="1393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1393
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<td class="diff-line-num new_line" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1553
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<pre style="margin: 0;"> <span id="LC1553" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1394
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<td class="diff-line-num new_line" data-linenumber="1554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1554
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<pre style="margin: 0;"> <span id="LC1554" class="line" lang="plaintext">.BI \-\-fastq_minlen\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1395
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<td class="diff-line-num new_line" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1555
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<pre style="margin: 0;"> <span id="LC1555" class="line" lang="plaintext">When using \-\-fastq_filter, \-\-fastq_mergepairs or \-\-fastx_filter,</span>
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<td class="diff-line-num old_line" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1396
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<td class="diff-line-num new_line" data-linenumber="1556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1556
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<pre style="margin: 0;"> <span id="LC1556" class="line" lang="plaintext">discard sequences with less than the specified number of bases</span>
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<td class="diff-line-num old_line" data-linenumber="1397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1397
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1557
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<pre style="margin: 0;"> <span id="LC1557" class="line" lang="plaintext">(default 1).</span>
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<td class="diff-line-num new old_line" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1558
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<pre style="margin: 0;">+<span id="LC1558" class="line" lang="plaintext">.TAG fastq_minmergelen</span>
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1398
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1559
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<pre style="margin: 0;"> <span id="LC1559" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1399
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1560
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<pre style="margin: 0;"> <span id="LC1560" class="line" lang="plaintext">.BI \-\-fastq_minmergelen\~ "positive integer"</span>
</pre>
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1400
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<td class="diff-line-num 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">
1561
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<pre style="margin: 0;"> <span id="LC1561" class="line" lang="plaintext">When using \-\-fastq_mergepairs, specify the minimum length of the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1401
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1562
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<pre style="margin: 0;"> <span id="LC1562" class="line" lang="plaintext">merged sequence. The default is 1.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1563
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<pre style="margin: 0;">+<span id="LC1563" class="line" lang="plaintext">.TAG fastq_minovlen</span>
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1402
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1564
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<pre style="margin: 0;"> <span id="LC1564" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1403
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<td class="diff-line-num new_line" data-linenumber="1565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1565
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<pre style="margin: 0;"> <span id="LC1565" class="line" lang="plaintext">.BI \-\-fastq_minovlen\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1404
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<td class="diff-line-num new_line" data-linenumber="1566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1566
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<pre style="margin: 0;"> <span id="LC1566" class="line" lang="plaintext">When using \-\-fastq_mergepairs, specify the minimum overlap between</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1405
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<td class="diff-line-num new_line" data-linenumber="1567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1567
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<pre style="margin: 0;"> <span id="LC1567" class="line" lang="plaintext">the merged reads. The default is 10.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); 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="1568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1568
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<pre style="margin: 0;">+<span id="LC1568" class="line" lang="plaintext">.TAG fastq_nostagger</span>
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<td class="diff-line-num old_line" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1406
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<td class="diff-line-num new_line" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1569
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<pre style="margin: 0;"> <span id="LC1569" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1407
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<td class="diff-line-num new_line" data-linenumber="1570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1570
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<pre style="margin: 0;"> <span id="LC1570" class="line" lang="plaintext">.B \-\-fastq_nostagger</span>
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<td class="diff-line-num old_line" data-linenumber="1408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1408
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<td class="diff-line-num new_line" data-linenumber="1571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1571
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<pre style="margin: 0;"> <span id="LC1571" class="line" lang="plaintext">When using \-\-fastq_mergepairs, forbid the merging of staggered read</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1409
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<td class="diff-line-num new_line" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1572
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1572" class="line" lang="plaintext">pairs. This is the default behaviour of \-\-fastq_mergepairs. To</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1410
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<td class="diff-line-num new_line" data-linenumber="1573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1573
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<pre style="margin: 0;"> <span id="LC1573" class="line" lang="plaintext">change that behaviour, see the \-\-fastq_allowmergestagger option.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); 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="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1574
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<pre style="margin: 0;">+<span id="LC1574" class="line" lang="plaintext">.TAG fastq_qmax</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1411
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<td class="diff-line-num new_line" data-linenumber="1575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1575
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1575" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1412
</td>
<td class="diff-line-num new_line" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1576
</td>
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<pre style="margin: 0;"> <span id="LC1576" class="line" lang="plaintext">.BI \-\-fastq_qmax\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1413
</td>
<td class="diff-line-num new_line" data-linenumber="1577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1577
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1577" class="line" lang="plaintext">Specify the maximum quality score accepted when reading FASTQ</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="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1414
</td>
<td class="diff-line-num new_line" data-linenumber="1578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1578
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1578" class="line" lang="plaintext">files. The default is 41, which is usual for recent Sanger/Illumina</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1415
</td>
<td class="diff-line-num new_line" data-linenumber="1579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1579
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1579" class="line" lang="plaintext">1.8+ files.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1580
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<pre style="margin: 0;">+<span id="LC1580" class="line" lang="plaintext">.TAG fastq_qmaxout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1416
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<td class="diff-line-num new_line" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1581
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1581" class="line" lang="plaintext">.TP</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="1417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1417
</td>
<td class="diff-line-num new_line" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1582
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1582" class="line" lang="plaintext">.BI \-\-fastq_qmaxout\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1418
</td>
<td class="diff-line-num new_line" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1583
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1583" class="line" lang="plaintext">When using \-\-fastq_convert or \-\-sff_convert, specify the maximum</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1419
</td>
<td class="diff-line-num new_line" data-linenumber="1584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1584
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1584" class="line" lang="plaintext">quality score used when writing FASTQ files. The default is 41, which</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="1420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1420
</td>
<td class="diff-line-num new_line" data-linenumber="1585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1585
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1421
</td>
<td class="diff-line-num new_line" data-linenumber="1586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1586
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1586" class="line" lang="plaintext">a maximum quality score of 40.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1587
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<pre style="margin: 0;">+<span id="LC1587" class="line" lang="plaintext">.TAG fastq_qmin</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1422
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<td class="diff-line-num new_line" data-linenumber="1588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1588
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1588" class="line" lang="plaintext">.TP</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="1423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1423
</td>
<td class="diff-line-num new_line" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1589
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1589" class="line" lang="plaintext">.BI \-\-fastq_qmin\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1424
</td>
<td class="diff-line-num new_line" data-linenumber="1590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1590
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1590" class="line" lang="plaintext">Specify the minimum quality score accepted for FASTQ files. The</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1425
</td>
<td class="diff-line-num new_line" data-linenumber="1591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1591
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1591" class="line" lang="plaintext">default is 0, which is usual for recent Sanger/Illumina 1.8+</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1426
</td>
<td class="diff-line-num new_line" data-linenumber="1592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1592
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1592" class="line" lang="plaintext">files. Older formats may use scores between -5 and 2.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1593
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<pre style="margin: 0;">+<span id="LC1593" class="line" lang="plaintext">.TAG fastq_qminout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1427
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<td class="diff-line-num new_line" data-linenumber="1594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1594
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1594" class="line" lang="plaintext">.TP</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="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1428
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<td class="diff-line-num new_line" data-linenumber="1595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1595
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1595" class="line" lang="plaintext">.BI \-\-fastq_qminout\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1429
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<td class="diff-line-num new_line" data-linenumber="1596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1596
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1596" class="line" lang="plaintext">When using \-\-fastq_convert or \-\-sff_convert, specify the minimum</span>
</pre>
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1430
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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_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1431
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<td class="diff-line-num new_line" data-linenumber="1598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1598
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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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<td class="diff-line-num old_line" data-linenumber="1432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1432
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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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<td class="diff-line-num new old_line" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1600
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<pre style="margin: 0;">+<span id="LC1600" class="line" lang="plaintext">.TAG fastq_stats</span>
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<td class="diff-line-num old_line" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1433
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<td class="diff-line-num new_line" data-linenumber="1601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1601
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<pre style="margin: 0;"> <span id="LC1601" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1434
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<td class="diff-line-num new_line" data-linenumber="1602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1602
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<pre style="margin: 0;"> <span id="LC1602" class="line" lang="plaintext">.BI \-\-fastq_stats \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1435
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<td class="diff-line-num new_line" data-linenumber="1603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1603
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<pre style="margin: 0;"> <span id="LC1603" class="line" lang="plaintext">Analyze a FASTQ file and report the number of reads it contains. The</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1513" style="width: 35px; color: rgba(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="1681" style="width: 35px; color: rgba(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">@@ -1513,63 +1681,77 @@ position with a quality \fIQ\fR below 5, 10, 15 or 20 (option</td>
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<td class="diff-line-num old_line" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1513
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<td class="diff-line-num new_line" data-linenumber="1681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1681
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<pre style="margin: 0;"> <span id="LC1681" class="line" lang="plaintext">\-\-fastq_truncqual \fIQ\fR).</span>
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<td class="diff-line-num old_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1514
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<td class="diff-line-num new_line" data-linenumber="1682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1682
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<pre style="margin: 0;"> <span id="LC1682" class="line" lang="plaintext">.RE</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1515
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<td class="diff-line-num new_line" data-linenumber="1683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1683
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<pre style="margin: 0;"> <span id="LC1683" class="line" lang="plaintext">.RE</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1684
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<pre style="margin: 0;">+<span id="LC1684" class="line" lang="plaintext">.TAG fastq_stripleft</span>
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<td class="diff-line-num old_line" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1516
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<td class="diff-line-num new_line" data-linenumber="1685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1685
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1685" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1517
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<td class="diff-line-num new_line" data-linenumber="1686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1686
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<pre style="margin: 0;"> <span id="LC1686" class="line" lang="plaintext">.BI \-\-fastq_stripleft\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1518
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<td class="diff-line-num new_line" data-linenumber="1687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1687
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<pre style="margin: 0;"> <span id="LC1687" class="line" lang="plaintext">When using \-\-fastq_filter or \-\-fastx_filter, strip the specified</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1519
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<td class="diff-line-num new_line" data-linenumber="1688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1688
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1688" class="line" lang="plaintext">number of bases from the left end of the reads.</span>
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<td class="diff-line-num new old_line" data-linenumber="1520" style="width: 35px; color: rgba(0,0,0,0.3); 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="1689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1689
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<pre style="margin: 0;">+<span id="LC1689" class="line" lang="plaintext">.TAG fastq_stripright</span>
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<td class="diff-line-num old_line" data-linenumber="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1520
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<td class="diff-line-num new_line" data-linenumber="1690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1690
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<pre style="margin: 0;"> <span id="LC1690" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1521
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<td class="diff-line-num new_line" data-linenumber="1691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1691
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<pre style="margin: 0;"> <span id="LC1691" class="line" lang="plaintext">.BI \-\-fastq_stripright\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1522
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<td class="diff-line-num new_line" data-linenumber="1692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1692
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<pre style="margin: 0;"> <span id="LC1692" class="line" lang="plaintext">When using \-\-fastq_filter or \-\-fastx_filter, strip the specified</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1523
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<td class="diff-line-num new_line" data-linenumber="1693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1693
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<pre style="margin: 0;"> <span id="LC1693" class="line" lang="plaintext">number of bases from the right end of the reads.</span>
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<td class="diff-line-num new old_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); 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="1694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1694
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<pre style="margin: 0;">+<span id="LC1694" class="line" lang="plaintext">.TAG fastq_tail</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1524
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<td class="diff-line-num new_line" data-linenumber="1695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1695
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<pre style="margin: 0;"> <span id="LC1695" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1525
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<td class="diff-line-num new_line" data-linenumber="1696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1696
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<pre style="margin: 0;"> <span id="LC1696" class="line" lang="plaintext">.BI \-\-fastq_tail\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1526
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<td class="diff-line-num new_line" data-linenumber="1697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1697
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<pre style="margin: 0;"> <span id="LC1697" class="line" lang="plaintext">When using \-\-fastq_chars, count the number of times a series of</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1527
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<td class="diff-line-num new_line" data-linenumber="1698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1698
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<pre style="margin: 0;"> <span id="LC1698" class="line" lang="plaintext">characters of length \fIk\fR appears at the end of quality strings. By</span>
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<td class="diff-line-num old_line" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1528
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<td class="diff-line-num new_line" data-linenumber="1699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1699
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<pre style="margin: 0;"> <span id="LC1699" class="line" lang="plaintext">default, \fIk\fR = 4.</span>
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<td class="diff-line-num new old_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); 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="1700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1700
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<pre style="margin: 0;">+<span id="LC1700" class="line" lang="plaintext">.TAG fastq_truncee</span>
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<td class="diff-line-num old_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1529
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<td class="diff-line-num new_line" data-linenumber="1701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1701
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<pre style="margin: 0;"> <span id="LC1701" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1530
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<td class="diff-line-num new_line" data-linenumber="1702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1702
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<pre style="margin: 0;"> <span id="LC1702" class="line" lang="plaintext">.BI \-\-fastq_truncee\~ real</span>
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<td class="diff-line-num old_line" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1531
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<td class="diff-line-num new_line" data-linenumber="1703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1703
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<pre style="margin: 0;"> <span id="LC1703" class="line" lang="plaintext">When using \-\-fastq_filter or \-\-fastx_filter, truncate sequences so</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1532
</td>
<td class="diff-line-num new_line" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1704
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<pre style="margin: 0;"> <span id="LC1704" class="line" lang="plaintext">that their total expected error is not higher than the specified</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1533
</td>
<td class="diff-line-num new_line" data-linenumber="1705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1705
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1705" class="line" lang="plaintext">value.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1706
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<pre style="margin: 0;">+<span id="LC1706" class="line" lang="plaintext">.TAG fastq_trunclen</span>
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<td class="diff-line-num old_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1534
</td>
<td class="diff-line-num new_line" data-linenumber="1707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1707
</td>
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<pre style="margin: 0;"> <span id="LC1707" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1535
</td>
<td class="diff-line-num new_line" data-linenumber="1708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1708
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<pre style="margin: 0;"> <span id="LC1708" class="line" lang="plaintext">.BI \-\-fastq_trunclen\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1536
</td>
<td class="diff-line-num new_line" data-linenumber="1709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1709
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1709" class="line" lang="plaintext">When using \-\-fastq_filter or \-\-fastx_filter, truncate sequences to</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="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
</td>
<td class="diff-line-num new_line" data-linenumber="1710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1710
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1710" class="line" lang="plaintext">the specified length. Shorter sequences are discarded.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1711
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<pre style="margin: 0;">+<span id="LC1711" class="line" lang="plaintext">.TAG fastq_trunclen_keep</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1538
</td>
<td class="diff-line-num new_line" data-linenumber="1712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1712
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1712" class="line" lang="plaintext">.TP</span>
</pre>
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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
</td>
<td class="diff-line-num new_line" data-linenumber="1713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1713
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<pre style="margin: 0;"> <span id="LC1713" class="line" lang="plaintext">.BI \-\-fastq_trunclen_keep\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1540
</td>
<td class="diff-line-num new_line" data-linenumber="1714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1714
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1714" class="line" lang="plaintext">When using \-\-fastq_filter or \-\-fastx_filter, truncate sequences to</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="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1541
</td>
<td class="diff-line-num new_line" data-linenumber="1715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1715
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1715" class="line" lang="plaintext">the specified length. Shorter sequences are not discarded.</span>
</pre>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1716
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<pre style="margin: 0;">+<span id="LC1716" class="line" lang="plaintext">.TAG fastq_truncqual</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1542
</td>
<td class="diff-line-num new_line" data-linenumber="1717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1717
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1717" class="line" lang="plaintext">.TP</span>
</pre>
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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
</td>
<td class="diff-line-num new_line" data-linenumber="1718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1718
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<pre style="margin: 0;"> <span id="LC1718" class="line" lang="plaintext">.BI \-\-fastq_truncqual\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1544
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<td class="diff-line-num new_line" data-linenumber="1719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1719
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1719" class="line" lang="plaintext">When using \-\-fastq_filter or \-\-fastx_filter, truncate sequences</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<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
</td>
<td class="diff-line-num new_line" data-linenumber="1720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1720
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1720" class="line" lang="plaintext">starting from the first base with the specified base quality score</span>
</pre>
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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
</td>
<td class="diff-line-num new_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1721
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1721" class="line" lang="plaintext">value or lower.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1722
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<pre style="margin: 0;">+<span id="LC1722" class="line" lang="plaintext">.TAG fastqout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1547
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<td class="diff-line-num new_line" data-linenumber="1723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1723
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1723" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1548
</td>
<td class="diff-line-num new_line" data-linenumber="1724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1724
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1724" class="line" lang="plaintext">.BI \-\-fastqout \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1549
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<td class="diff-line-num new_line" data-linenumber="1725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1725
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<pre style="margin: 0;"> <span id="LC1725" class="line" lang="plaintext">When using \-\-fastq_filter, \-\-fastq_mergepairs or \-\-fastx_filter,</span>
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<td class="diff-line-num old_line" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1550
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<td class="diff-line-num new_line" data-linenumber="1726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1726
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<pre style="margin: 0;"> <span id="LC1726" class="line" lang="plaintext">write to the given FASTQ-formatted file the sequences passing the</span>
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<td class="diff-line-num old_line" data-linenumber="1551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1551
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<td class="diff-line-num new_line" data-linenumber="1727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1727
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<pre style="margin: 0;"> <span id="LC1727" class="line" lang="plaintext">filter, or the merged sequences.</span>
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<td class="diff-line-num new old_line" data-linenumber="1552" style="width: 35px; color: rgba(0,0,0,0.3); 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="1728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1728
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<pre style="margin: 0;">+<span id="LC1728" class="line" lang="plaintext">.TAG fastqout_rev</span>
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<td class="diff-line-num old_line" data-linenumber="1552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1552
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<td class="diff-line-num new_line" data-linenumber="1729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1729
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<pre style="margin: 0;"> <span id="LC1729" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1553
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<td class="diff-line-num new_line" data-linenumber="1730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1730
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<pre style="margin: 0;"> <span id="LC1730" class="line" lang="plaintext">.BI \-\-fastqout_rev \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1554
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<td class="diff-line-num new_line" data-linenumber="1731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1731
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<pre style="margin: 0;"> <span id="LC1731" class="line" lang="plaintext">When using \-\-fastq_filter or \-\-fastx_filter,</span>
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<td class="diff-line-num old_line" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1555
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<td class="diff-line-num new_line" data-linenumber="1732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1732
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<pre style="margin: 0;"> <span id="LC1732" class="line" lang="plaintext">write to the given FASTQ-formatted file the reverse reads passing the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1556
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<td class="diff-line-num new_line" data-linenumber="1733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1733
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<pre style="margin: 0;"> <span id="LC1733" class="line" lang="plaintext">filter.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1734
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<pre style="margin: 0;">+<span id="LC1734" class="line" lang="plaintext">.TAG fastqout_discarded</span>
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<td class="diff-line-num old_line" data-linenumber="1557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1557
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<td class="diff-line-num new_line" data-linenumber="1735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1735
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<pre style="margin: 0;"> <span id="LC1735" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1558
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<td class="diff-line-num new_line" data-linenumber="1736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1736
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<pre style="margin: 0;"> <span id="LC1736" class="line" lang="plaintext">.BI \-\-fastqout_discarded \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1559
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<td class="diff-line-num new_line" data-linenumber="1737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1737
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<pre style="margin: 0;"> <span id="LC1737" class="line" lang="plaintext">When using \-\-fastq_filter or \-\-fastx_filter, write sequences that</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1560
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<td class="diff-line-num new_line" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1738
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<pre style="margin: 0;"> <span id="LC1738" class="line" lang="plaintext">do not pass the filter to the given FASTQ-formatted file.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1739
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<pre style="margin: 0;">+<span id="LC1739" class="line" lang="plaintext">.TAG fastqout_discarded_rev</span>
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<td class="diff-line-num old_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">
1561
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<td class="diff-line-num new_line" data-linenumber="1740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1740
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<pre style="margin: 0;"> <span id="LC1740" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1562
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<td class="diff-line-num new_line" data-linenumber="1741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1741
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<pre style="margin: 0;"> <span id="LC1741" class="line" lang="plaintext">.BI \-\-fastqout_discarded_rev \0filename</span>
</pre>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="1742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1742
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<pre style="margin: 0;"> <span id="LC1742" class="line" lang="plaintext">When using \-\-fastq_filter or \-\-fastx_filter, write reverse reads that</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1564
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<td class="diff-line-num new_line" data-linenumber="1743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1743
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<pre style="margin: 0;"> <span id="LC1743" class="line" lang="plaintext">do not pass the filter to the given FASTQ-formatted file.</span>
</pre>
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<td class="diff-line-num new old_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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1744
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<pre style="margin: 0;">+<span id="LC1744" class="line" lang="plaintext">.TAG fastqout_notmerged_fwd</span>
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<td class="diff-line-num old_line" data-linenumber="1565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1565
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<td class="diff-line-num new_line" data-linenumber="1745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1745
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1745" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1566
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<td class="diff-line-num new_line" data-linenumber="1746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1746
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<pre style="margin: 0;"> <span id="LC1746" class="line" lang="plaintext">.BI \-\-fastqout_notmerged_fwd \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1567
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<td class="diff-line-num new_line" data-linenumber="1747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1747
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<pre style="margin: 0;"> <span id="LC1747" class="line" lang="plaintext">When using \-\-fastq_mergepairs, write forward reads not merged to the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1568
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<td class="diff-line-num new_line" data-linenumber="1748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1748
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<pre style="margin: 0;"> <span id="LC1748" class="line" lang="plaintext">specified FASTQ file.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); 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="1749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1749
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<pre style="margin: 0;">+<span id="LC1749" class="line" lang="plaintext">.TAG fastqout_notmerged_rev</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1569
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<td class="diff-line-num new_line" data-linenumber="1750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1750
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<pre style="margin: 0;"> <span id="LC1750" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1570
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<td class="diff-line-num new_line" data-linenumber="1751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1751
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<pre style="margin: 0;"> <span id="LC1751" class="line" lang="plaintext">.BI \-\-fastqout_notmerged_rev \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1571
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<td class="diff-line-num new_line" data-linenumber="1752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1752
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<pre style="margin: 0;"> <span id="LC1752" class="line" lang="plaintext">When using \-\-fastq_mergepairs, write reverse reads not merged to the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1572
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<td class="diff-line-num new_line" data-linenumber="1753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1753
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<pre style="margin: 0;"> <span id="LC1753" class="line" lang="plaintext">specified FASTQ file.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1573" style="width: 35px; color: rgba(0,0,0,0.3); 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="1754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1754
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<pre style="margin: 0;">+<span id="LC1754" class="line" lang="plaintext">.TAG fastx_filter</span>
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<td class="diff-line-num old_line" data-linenumber="1573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1573
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<td class="diff-line-num new_line" data-linenumber="1755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1755
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<pre style="margin: 0;"> <span id="LC1755" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1574
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<td class="diff-line-num new_line" data-linenumber="1756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1756
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<pre style="margin: 0;"> <span id="LC1756" class="line" lang="plaintext">.BI \-\-fastx_filter \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1575
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<td class="diff-line-num new_line" data-linenumber="1757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1757
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<pre style="margin: 0;"> <span id="LC1757" class="line" lang="plaintext">Trim and/or filter the sequences in the given FASTA or FASTQ file and</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1600" style="width: 35px; color: rgba(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="1782" style="width: 35px; color: rgba(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">@@ -1600,61 +1782,79 @@ relabel the output sequences. The \-\-eeout option may be used to output the</td>
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<td class="diff-line-num old_line" data-linenumber="1600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1600
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<td class="diff-line-num new_line" data-linenumber="1782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1782
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<pre style="margin: 0;"> <span id="LC1782" class="line" lang="plaintext">expected number of errors in each sequence. After all sequences have</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1601
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<td class="diff-line-num new_line" data-linenumber="1783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1783
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<pre style="margin: 0;"> <span id="LC1783" class="line" lang="plaintext">been processed, the number of kept and discarded sequences will be</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1602
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<td class="diff-line-num new_line" data-linenumber="1784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1784
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<pre style="margin: 0;"> <span id="LC1784" class="line" lang="plaintext">shown, as well as how many of the kept sequences were trimmed.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1603" style="width: 35px; color: rgba(0,0,0,0.3); 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="1785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1785
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<pre style="margin: 0;">+<span id="LC1785" class="line" lang="plaintext">.TAG fastx_revcomp</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1603
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<td class="diff-line-num new_line" data-linenumber="1786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1786
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1786" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1604
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<td class="diff-line-num new_line" data-linenumber="1787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1787
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<pre style="margin: 0;"> <span id="LC1787" class="line" lang="plaintext">.BI \-\-fastx_revcomp \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1605
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<td class="diff-line-num new_line" data-linenumber="1788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1788
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1788" class="line" lang="plaintext">Reverse-complement the sequences in the given FASTA or FASTQ file to a</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1606
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<td class="diff-line-num new_line" data-linenumber="1789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1789
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<pre style="margin: 0;"> <span id="LC1789" class="line" lang="plaintext">file specified with the \-\-fastaout and/or \-\-fastqout options. If</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1607
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<td class="diff-line-num new_line" data-linenumber="1790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1790
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<pre style="margin: 0;"> <span id="LC1790" class="line" lang="plaintext">the input file is in FASTA format, the output can not be written back</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1608
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<td class="diff-line-num new_line" data-linenumber="1791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1791
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<pre style="margin: 0;"> <span id="LC1791" class="line" lang="plaintext">to a FASTQ file due to missing base quality scores.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1609" style="width: 35px; color: rgba(0,0,0,0.3); 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="1792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1792
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<pre style="margin: 0;">+<span id="LC1792" class="line" lang="plaintext">.TAG join_padgap</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1609
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<td class="diff-line-num new_line" data-linenumber="1793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1793
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<pre style="margin: 0;"> <span id="LC1793" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1610
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<td class="diff-line-num new_line" data-linenumber="1794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1794
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<pre style="margin: 0;"> <span id="LC1794" class="line" lang="plaintext">.BI \-\-join_padgap\~ string</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1611
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<td class="diff-line-num new_line" data-linenumber="1795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1795
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1795" class="line" lang="plaintext">When running \-\-fastq_join, use the \fIstring\fR as a sequence</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1612
</td>
<td class="diff-line-num new_line" data-linenumber="1796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1796
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1796" class="line" lang="plaintext">padding string. The default is NNNNNNNN (8 N's).</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1797
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<pre style="margin: 0;">+<span id="LC1797" class="line" lang="plaintext">.TAG join_padgapq</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1613
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<td class="diff-line-num new_line" data-linenumber="1798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1798
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1798" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1614
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<td class="diff-line-num new_line" data-linenumber="1799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1799
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1799" class="line" lang="plaintext">.BI \-\-join_padgapq\~ string</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1615
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<td class="diff-line-num new_line" data-linenumber="1800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1800
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<pre style="margin: 0;"> <span id="LC1800" class="line" lang="plaintext">When running \-\-fastq_join, use the \fIstring\fR as a quality padding</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1616
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<td class="diff-line-num new_line" data-linenumber="1801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1801
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<pre style="margin: 0;"> <span id="LC1801" class="line" lang="plaintext">string. The default is a string of I's equal in length to the sequence</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1617
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<td class="diff-line-num new_line" data-linenumber="1802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1802
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<pre style="margin: 0;"> <span id="LC1802" class="line" lang="plaintext">padding string. The letter I corresponds to a base quality score of 40</span>
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<td class="diff-line-num old_line" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1618
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<td class="diff-line-num new_line" data-linenumber="1803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1803
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<pre style="margin: 0;"> <span id="LC1803" class="line" lang="plaintext">indicating a very high quality base with error probability of 0.0001.</span>
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<td class="diff-line-num new old_line" data-linenumber="1619" style="width: 35px; color: rgba(0,0,0,0.3); 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="1804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1804
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<pre style="margin: 0;">+<span id="LC1804" class="line" lang="plaintext">.TAG label_suffix</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1619
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<td class="diff-line-num new_line" data-linenumber="1805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1805
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<pre style="margin: 0;"> <span id="LC1805" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1620
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<td class="diff-line-num new_line" data-linenumber="1806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1806
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<pre style="margin: 0;"> <span id="LC1806" class="line" lang="plaintext">.BI \-\-label_suffix\~ string</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1621
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<td class="diff-line-num new_line" data-linenumber="1807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1807
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<pre style="margin: 0;"> <span id="LC1807" class="line" lang="plaintext">When using \-\-fastx_revcomp or \-\-fastq_mergepairs, add the suffix</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1622
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<td class="diff-line-num new_line" data-linenumber="1808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1808
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<pre style="margin: 0;"> <span id="LC1808" class="line" lang="plaintext">\fIstring\fR to sequence headers.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1809
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<pre style="margin: 0;">+<span id="LC1809" class="line" lang="plaintext">.TAG maxsize</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1623
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<td class="diff-line-num new_line" data-linenumber="1810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1810
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<pre style="margin: 0;"> <span id="LC1810" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1624
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<td class="diff-line-num new_line" data-linenumber="1811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1811
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<pre style="margin: 0;"> <span id="LC1811" class="line" lang="plaintext">.BI \-\-maxsize\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1625
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<td class="diff-line-num new_line" data-linenumber="1812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1812
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<pre style="margin: 0;"> <span id="LC1812" class="line" lang="plaintext">When using \-\-fastq_filter or \-\-fastx_filter, discard sequences</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1626
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<td class="diff-line-num new_line" data-linenumber="1813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1813
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1813" class="line" lang="plaintext">with an abundance higher than the specified value.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1814
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<pre style="margin: 0;">+<span id="LC1814" class="line" lang="plaintext">.TAG minsize</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1627
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<td class="diff-line-num new_line" data-linenumber="1815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1815
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1815" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1628
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<td class="diff-line-num new_line" data-linenumber="1816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1816
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<pre style="margin: 0;"> <span id="LC1816" class="line" lang="plaintext">.BI \-\-minsize\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1629
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<td class="diff-line-num new_line" data-linenumber="1817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1817
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1817" class="line" lang="plaintext">When using \-\-fastq_filter or \-\-fastx_filter, discard sequences</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1630
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<td class="diff-line-num new_line" data-linenumber="1818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1818
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1818" class="line" lang="plaintext">with an abundance lower than the specified value.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1819
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<pre style="margin: 0;">+<span id="LC1819" class="line" lang="plaintext">.TAG output</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1631
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<td class="diff-line-num new_line" data-linenumber="1820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1820
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1820" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1632
</td>
<td class="diff-line-num new_line" data-linenumber="1821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1821
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1821" class="line" lang="plaintext">.BI \-\-output \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1633
</td>
<td class="diff-line-num new_line" data-linenumber="1822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1822
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1822" class="line" lang="plaintext">When using \-\-fastq_eestats or \-\-fastq_eestats2, write tabulated</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="1634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1634
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<td class="diff-line-num new_line" data-linenumber="1823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1823
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1823" class="line" lang="plaintext">results to \fIfilename\fR. See \-\-fastq_eestats's and</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1635
</td>
<td class="diff-line-num new_line" data-linenumber="1824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1824
</td>
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<pre style="margin: 0;"> <span id="LC1824" class="line" lang="plaintext">\-\-fastq_eestats2's documentation for a complete description of the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1636
</td>
<td class="diff-line-num new_line" data-linenumber="1825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1825
</td>
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<pre style="margin: 0;"> <span id="LC1825" class="line" lang="plaintext">table.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1826
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<pre style="margin: 0;">+<span id="LC1826" class="line" lang="plaintext">.TAG relabel_keep</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1637
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<td class="diff-line-num new_line" data-linenumber="1827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1827
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1827" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1638
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<td class="diff-line-num new_line" data-linenumber="1828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1828
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1828" class="line" lang="plaintext">.B \-\-relabel_keep</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1639
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<td class="diff-line-num new_line" data-linenumber="1829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1829
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1829" class="line" lang="plaintext">When using \-\-relabel, keep the old identifier in the header after a</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1640
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<td class="diff-line-num new_line" data-linenumber="1830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1830
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<pre style="margin: 0;"> <span id="LC1830" class="line" lang="plaintext">space.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1831
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<pre style="margin: 0;">+<span id="LC1831" class="line" lang="plaintext">.TAG relabel</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1641
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<td class="diff-line-num new_line" data-linenumber="1832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1832
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1832" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1642
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<td class="diff-line-num new_line" data-linenumber="1833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1833
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1833" class="line" lang="plaintext">.BI \-\-relabel \0string</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1643
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<td class="diff-line-num new_line" data-linenumber="1834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1834
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1834" class="line" lang="plaintext">Please see the description of the same option under Chimera detection</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1644
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<td class="diff-line-num new_line" data-linenumber="1835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1835
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1835" class="line" lang="plaintext">for details.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1836
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<pre style="margin: 0;">+<span id="LC1836" class="line" lang="plaintext">.TAG relabel_md5</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1645
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<td class="diff-line-num new_line" data-linenumber="1837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1837
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1837" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1646
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<td class="diff-line-num new_line" data-linenumber="1838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1838
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1838" class="line" lang="plaintext">.BI \-\-relabel_md5</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1647
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<td class="diff-line-num new_line" data-linenumber="1839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1839
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1839" class="line" lang="plaintext">Please see the description of the same option under Chimera detection</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1648
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<td class="diff-line-num new_line" data-linenumber="1840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1840
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1840" class="line" lang="plaintext">for details.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); 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="1841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1841
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<pre style="margin: 0;">+<span id="LC1841" class="line" lang="plaintext">.TAG relabel_self</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); 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="1842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1842
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<pre style="margin: 0;">+<span id="LC1842" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1843
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<pre style="margin: 0;">+<span id="LC1843" class="line" lang="plaintext">.BI \-\-relabel_self</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); 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="1844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1844
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<pre style="margin: 0;">+<span id="LC1844" class="line" lang="plaintext">Please see the description of the same option under Chimera detection</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); 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="1845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1845
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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="LC1845" class="line" lang="plaintext">for details.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); 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="1846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1846
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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="LC1846" class="line" lang="plaintext">.TAG relabel_sha1</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1649
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<td class="diff-line-num new_line" data-linenumber="1847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1847
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1847" class="line" lang="plaintext">.TP</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="1650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1650
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<td class="diff-line-num new_line" data-linenumber="1848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1848
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1848" class="line" lang="plaintext">.BI \-\-relabel_sha1</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1651
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<td class="diff-line-num new_line" data-linenumber="1849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1849
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1849" class="line" lang="plaintext">Please see the description of the same option under Chimera detection</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1652
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<td class="diff-line-num new_line" data-linenumber="1850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1850
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1850" class="line" lang="plaintext">for details.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1653" style="width: 35px; color: rgba(0,0,0,0.3); 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="1851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1851
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<pre style="margin: 0;">+<span id="LC1851" class="line" lang="plaintext">.TAG reverse</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1653
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1852
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<pre style="margin: 0;"> <span id="LC1852" class="line" lang="plaintext">.TP</span>
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1654
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1853
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<pre style="margin: 0;"> <span id="LC1853" class="line" lang="plaintext">.BI \-\-reverse \0filename</span>
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1655
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1854
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<pre style="margin: 0;"> <span id="LC1854" class="line" lang="plaintext">When using \-\-fastq_filter, \-\-fastx_filter, \-\-fastq_mergepairs or</span>
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1656
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1855
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<pre style="margin: 0;"> <span id="LC1855" class="line" lang="plaintext">\-\-fastq_join, specify the FASTQ file containing containing the</span>
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1657
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1856
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<pre style="margin: 0;"> <span id="LC1856" class="line" lang="plaintext">reverse reads.</span>
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1857
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<pre style="margin: 0;">+<span id="LC1857" class="line" lang="plaintext">.TAG sff_convert</span>
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1658
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1858
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<pre style="margin: 0;"> <span id="LC1858" class="line" lang="plaintext">.TP</span>
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1659
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1859
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<pre style="margin: 0;"> <span id="LC1859" class="line" lang="plaintext">.BI \-\-sff_convert \0filename</span>
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1660
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1860
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<pre style="margin: 0;"> <span id="LC1860" class="line" lang="plaintext">Convert the given SFF file to FASTQ. The FASTQ output file is</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1665" style="width: 35px; color: rgba(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">@@ -1665,15 +1865,18 @@ converted to lower case, while the rest is in upper case. The output</td>
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1665
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1865
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<pre style="margin: 0;"> <span id="LC1865" class="line" lang="plaintext">quality encoding may be specified with the \-\-fastq_asciiout option</span>
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<td class="diff-line-num old_line" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1666
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1866
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<pre style="margin: 0;"> <span id="LC1866" class="line" lang="plaintext">(default 33). The minimum and maximum output quality scores may be</span>
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1667
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1867
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<pre style="margin: 0;"> <span id="LC1867" class="line" lang="plaintext">limited using the \-\-fastq_qminout and \-\-fastq_qmaxout options.</span>
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1868
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<pre style="margin: 0;">+<span id="LC1868" class="line" lang="plaintext">.TAG sff_clip</span>
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1668
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1869
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<pre style="margin: 0;"> <span id="LC1869" class="line" lang="plaintext">.TP</span>
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1669
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1870
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<pre style="margin: 0;"> <span id="LC1870" class="line" lang="plaintext">.BI \-\-sff_clip</span>
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1670
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1871
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<pre style="margin: 0;"> <span id="LC1871" class="line" lang="plaintext">Specifies that the sequences converted by the \-\-sff_convert command</span>
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1671
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1872
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<pre style="margin: 0;"> <span id="LC1872" class="line" lang="plaintext">should be clipped in both ends as indicated in the SFF file. By</span>
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1672
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1873
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<pre style="margin: 0;"> <span id="LC1873" class="line" lang="plaintext">default no clipping is performed.</span>
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1874
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<pre style="margin: 0;">+<span id="LC1874" class="line" lang="plaintext">.TAG xsize</span>
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1673
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1875
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<pre style="margin: 0;"> <span id="LC1875" class="line" lang="plaintext">.TP</span>
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1674
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1876
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<pre style="margin: 0;"> <span id="LC1876" class="line" lang="plaintext">.B \-\-xsize</span>
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1675
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1877
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<pre style="margin: 0;"> <span id="LC1877" class="line" lang="plaintext">Strip abundance information from the headers when writing the output</span>
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1676
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1878
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<pre style="margin: 0;"> <span id="LC1878" class="line" lang="plaintext">file.</span>
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1879
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<pre style="margin: 0;">+<span id="LC1879" class="line" lang="plaintext">.TAG xee</span>
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1677
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1880
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<pre style="margin: 0;"> <span id="LC1880" class="line" lang="plaintext">.TP</span>
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1678
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1881
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<pre style="margin: 0;"> <span id="LC1881" class="line" lang="plaintext">.B \-\-xee</span>
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1679
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1882
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<pre style="margin: 0;"> <span id="LC1882" class="line" lang="plaintext">Strip information about expected errors (ee) from the output file</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1885" style="width: 35px; color: rgba(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">@@ -1682,6 +1885,7 @@ headers. This information is added by the \-\-fastq_eeout and</td>
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1682
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1885
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<pre style="margin: 0;"> <span id="LC1885" class="line" lang="plaintext">.RE</span>
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1683
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1886
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<pre style="margin: 0;"> <span id="LC1886" class="line" lang="plaintext">.PP</span>
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1684
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1887
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<pre style="margin: 0;"> <span id="LC1887" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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1888
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<pre style="margin: 0;">+<span id="LC1888" class="line" lang="plaintext">.TAG masking-options</span>
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1685
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1889
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<pre style="margin: 0;"> <span id="LC1889" class="line" lang="plaintext">Masking options:</span>
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1686
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1890
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<pre style="margin: 0;"> <span id="LC1890" class="line" lang="plaintext">.RS</span>
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1687
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1891
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<pre style="margin: 0;"> <span id="LC1891" class="line" lang="plaintext">.PP</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">@@ -1689,70 +1893,87 @@ An input sequence can be composed of lower- or uppercase letters. When</td>
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1689
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1893
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<pre style="margin: 0;"> <span id="LC1893" class="line" lang="plaintext">soft masking is specified, lower case letters are treated as symbols</span>
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1690
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1894
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<pre style="margin: 0;"> <span id="LC1894" class="line" lang="plaintext">that should be masked. Otherwise the case of the input sequences is</span>
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1691
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1895
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<pre style="margin: 0;"> <span id="LC1895" class="line" lang="plaintext">ignored.</span>
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1692
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<pre style="margin: 0;">-<span id="LC1692" class="line" lang="plaintext">.<span class="idiff left right">br</span></span>
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1896
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<pre style="margin: 0;">+<span id="LC1896" class="line" lang="plaintext">.<span class="idiff left right">PP</span></span>
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1693
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1897
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<pre style="margin: 0;"> <span id="LC1897" class="line" lang="plaintext">Masking is performed by the commands for chimera detection</span>
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1694
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1898
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<pre style="margin: 0;"> <span id="LC1898" class="line" lang="plaintext">(uchime_denovo, uchime_ref), clustering (cluster_fast,</span>
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1695
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1899
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<pre style="margin: 0;"> <span id="LC1899" class="line" lang="plaintext">cluster_smallmem, cluster_size), masking (maskfasta, fastx_mask),</span>
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1696
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1900
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<pre style="margin: 0;"> <span id="LC1900" class="line" lang="plaintext">pairwise alignment (allpairs_global) and searching (search_exact,</span>
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1697
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1901
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<pre style="margin: 0;"> <span id="LC1901" class="line" lang="plaintext">usearch_global).</span>
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1698
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<pre style="margin: 0;">-<span id="LC1698" class="line" lang="plaintext">.<span class="idiff left right">br</span></span>
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1902
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<pre style="margin: 0;">+<span id="LC1902" class="line" lang="plaintext">.<span class="idiff left right">PP</span></span>
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1699
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1903
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<pre style="margin: 0;"> <span id="LC1903" class="line" lang="plaintext">Masking is usually specified with the \-\-qmask option, while the</span>
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1700
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1904
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<pre style="margin: 0;"> <span id="LC1904" class="line" lang="plaintext">\-\-dbmask option is used for the database sequences specified with</span>
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1701
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1905
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<pre style="margin: 0;"> <span id="LC1905" class="line" lang="plaintext">the \-\-db option with the \-\-usearch_global, \-\-search_exact and</span>
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1702
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1906
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<pre style="margin: 0;"> <span id="LC1906" class="line" lang="plaintext">\-\-uchime_ref commands.</span>
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1703
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<td class="diff-line-num new_line old" data-linenumber="1907" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1703" class="line" lang="plaintext">.<span class="idiff left right">br</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); 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="1907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1907
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<pre style="margin: 0;">+<span id="LC1907" class="line" lang="plaintext">.<span class="idiff left right">PP</span></span>
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<td class="diff-line-num old_line" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1704
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<td class="diff-line-num new_line" data-linenumber="1908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1908
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<pre style="margin: 0;"> <span id="LC1908" class="line" lang="plaintext">The argument to the \-\-qmask and \-\-dbmask option may be none, soft</span>
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<td class="diff-line-num old_line" data-linenumber="1705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1705
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<td class="diff-line-num new_line" data-linenumber="1909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1909
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<pre style="margin: 0;"> <span id="LC1909" class="line" lang="plaintext">or dust. If the argument is none, the no masking is performed. If the</span>
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<td class="diff-line-num old_line" data-linenumber="1706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1706
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<td class="diff-line-num new_line" data-linenumber="1910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1910
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<pre style="margin: 0;"> <span id="LC1910" class="line" lang="plaintext">argument is soft the lower case symbols are masked. Finally, if the</span>
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<td class="diff-line-num old_line" data-linenumber="1707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1707
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<td class="diff-line-num new_line" data-linenumber="1911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1911
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<pre style="margin: 0;"> <span id="LC1911" class="line" lang="plaintext">argument is dust, the sequence is masked using the DUST algorithm by</span>
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<td class="diff-line-num old_line" data-linenumber="1708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1708
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<td class="diff-line-num new_line" data-linenumber="1912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1912
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<pre style="margin: 0;"> <span id="LC1912" class="line" lang="plaintext">Tatusov and Lipman to mask low-complexity regions.</span>
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<td class="diff-line-num old old_line" data-linenumber="1709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1709
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<td class="diff-line-num new_line old" data-linenumber="1913" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1709" class="line" lang="plaintext">.<span class="idiff left right">br</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1710" style="width: 35px; color: rgba(0,0,0,0.3); 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="1913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1913
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<pre style="margin: 0;">+<span id="LC1913" class="line" lang="plaintext">.<span class="idiff left right">PP</span></span>
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<td class="diff-line-num old_line" data-linenumber="1710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1710
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<td class="diff-line-num new_line" data-linenumber="1914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1914
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<pre style="margin: 0;"> <span id="LC1914" class="line" lang="plaintext">If the \-\-hardmask option is specified, all masked regions are</span>
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<td class="diff-line-num old_line" data-linenumber="1711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1711
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<td class="diff-line-num new_line" data-linenumber="1915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1915
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<pre style="margin: 0;"> <span id="LC1915" class="line" lang="plaintext">converted to N's, otherwise masked regions are indicated by lower case</span>
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<td class="diff-line-num old_line" data-linenumber="1712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1712
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<td class="diff-line-num new_line" data-linenumber="1916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1916
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<pre style="margin: 0;"> <span id="LC1916" class="line" lang="plaintext">letters.</span>
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1713
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<pre style="margin: 0;">-<span id="LC1713" class="line" lang="plaintext">.<span class="idiff left right">br</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1917
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<pre style="margin: 0;">+<span id="LC1917" class="line" lang="plaintext">.<span class="idiff left right">PP</span></span>
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<td class="diff-line-num old_line" data-linenumber="1714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1714
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<td class="diff-line-num new_line" data-linenumber="1918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1918
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<pre style="margin: 0;"> <span id="LC1918" class="line" lang="plaintext">If any sequence is masked, the masked version of the sequence (with</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1715
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<td class="diff-line-num new_line" data-linenumber="1919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1919
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<pre style="margin: 0;"> <span id="LC1919" class="line" lang="plaintext">lower case letters or N's) is used in all output files. Otherwise the</span>
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<td class="diff-line-num old_line" data-linenumber="1716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1716
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<td class="diff-line-num new_line" data-linenumber="1920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1920
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<pre style="margin: 0;"> <span id="LC1920" class="line" lang="plaintext">sequence is unmodified. The exception is the sequences in the output</span>
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<td class="diff-line-num old_line" data-linenumber="1717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1717
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<td class="diff-line-num new_line" data-linenumber="1921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1921
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<pre style="margin: 0;"> <span id="LC1921" class="line" lang="plaintext">file specified with the \-\-uchimealns option, where the input</span>
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<td class="diff-line-num old_line" data-linenumber="1718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1718
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<td class="diff-line-num new_line" data-linenumber="1922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1922
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<pre style="margin: 0;"> <span id="LC1922" class="line" lang="plaintext">sequences are converted to upper case first and lower case letters</span>
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<td class="diff-line-num old_line" data-linenumber="1719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1719
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<td class="diff-line-num new_line" data-linenumber="1923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1923
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<pre style="margin: 0;"> <span id="LC1923" class="line" lang="plaintext">indicate disagreement between the aligned sequences.</span>
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1720
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<td class="diff-line-num new_line old" data-linenumber="1924" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1720" class="line" lang="plaintext">.br</span>
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<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1924
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<pre style="margin: 0;">+<span id="LC1924" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); 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="1925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1925
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<pre style="margin: 0;">+<span id="LC1925" class="line" lang="plaintext">The \-\-qmask option (or \-\-dbmask for database sequences) may be</span>
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<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); 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="1926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1926
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<pre style="margin: 0;">+<span id="LC1926" class="line" lang="plaintext">combined with the \-\-hardmask option. The results of using the none,</span>
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<td class="diff-line-num new new_line" data-linenumber="1927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1927
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<pre style="margin: 0;">+<span id="LC1927" class="line" lang="plaintext">dust or soft argument to \-\-qmask or \-\-dbmask are presented below,</span>
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1928
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<pre style="margin: 0;">+<span id="LC1928" class="line" lang="plaintext">assuming each input sequence contains both lower and uppercase</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1929
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1929" class="line" lang="plaintext">symbols.</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="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1930
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1930" class="line" lang="plaintext">.PP</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1931
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1931" class="line" lang="plaintext">Results if the \-\-hardmask option is off (default):</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1932
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1932" class="line" lang="plaintext">.RS</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1933
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1933" class="line" lang="plaintext">.TP 9</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1934
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1934" class="line" lang="plaintext">.B none:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1935
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1935" class="line" lang="plaintext">no masking, all symbols used, no change</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1936
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1936" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1937
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1937" class="line" lang="plaintext">.B dust:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1938
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1938" class="line" lang="plaintext">masked symbols lowercased, rest uppercased</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1939
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1939" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1940
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1940" class="line" lang="plaintext">.B soft:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1941
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1941" class="line" lang="plaintext">lowercase symbols masked, no case changes</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1942
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1942" class="line" lang="plaintext">.RE</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1943
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1943" class="line" lang="plaintext">.PP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1944
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1944" class="line" lang="plaintext">Results if the \-\-hardmask option is on:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1945
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1945" class="line" lang="plaintext">.RS</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1946
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1946" class="line" lang="plaintext">.TP 9</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1947
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1947" class="line" lang="plaintext">.B none:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1948
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1948" class="line" lang="plaintext">no masking, all symbols used, no change</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1949
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1949" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1950
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1950" class="line" lang="plaintext">.B dust:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1951
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1951" class="line" lang="plaintext">masked symbols changed to Ns, rest unchanged</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1952
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1952" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1953
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1953" class="line" lang="plaintext">.B soft:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1954
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1954" class="line" lang="plaintext">lowercase symbols masked and changed to Ns</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new new_line" data-linenumber="1955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1955
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<pre style="margin: 0;">+<span id="LC1955" class="line" lang="plaintext">.RE</span>
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<td class="diff-line-num new old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); 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="1956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1956
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<pre style="margin: 0;">+<span id="LC1956" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1721
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<td class="diff-line-num new_line" data-linenumber="1957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1957
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<pre style="margin: 0;"> <span id="LC1957" class="line" lang="plaintext">When a sequence region is masked, words in the region are not included</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1722
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<td class="diff-line-num new_line" data-linenumber="1958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1958
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<pre style="margin: 0;"> <span id="LC1958" class="line" lang="plaintext">in the indices used in the heuristic search algorithm. In all other</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1723
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<td class="diff-line-num new_line" data-linenumber="1959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1959
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1959" class="line" lang="plaintext">aspects, the region is treated as other regions.</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1724
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<td class="diff-line-num new_line old" data-linenumber="1960" style="width: 35px; color: rgba(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="LC1724" class="line" lang="plaintext">.<span class="idiff left right">br</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1725" style="width: 35px; color: rgba(0,0,0,0.3); 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="1960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1960
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<pre style="margin: 0;">+<span id="LC1960" class="line" lang="plaintext">.<span class="idiff left right">PP</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1725
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<td class="diff-line-num new_line" data-linenumber="1961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1961
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<pre style="margin: 0;"> <span id="LC1961" class="line" lang="plaintext">Regions in sequences that are hardmasked (with N's) have a zero</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1726
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<td class="diff-line-num new_line" data-linenumber="1962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1962
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<pre style="margin: 0;"> <span id="LC1962" class="line" lang="plaintext">alignment score and do not contribute to an alignment.</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1727
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<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(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="LC1727" class="line" lang="plaintext">.br</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1728
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<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(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="LC1728" class="line" lang="plaintext">Here are the results of combined masking options \-\-qmask (or</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1729
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(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="LC1729" class="line" lang="plaintext">\-\-dbmask for database sequences) and \-\-hardmask, assuming each</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1730
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(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="LC1730" class="line" lang="plaintext">input sequence contains both lower and uppercase nucleotides:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1731
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(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="LC1731" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1732
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(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="LC1732" class="line" lang="plaintext">.ce 10 \# center the table (10 lines)</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1733
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1733" class="line" lang="plaintext">.TS</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1734
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1734" class="line" lang="plaintext">tab(:);</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1735
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1735" class="line" lang="plaintext">c c c</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1736
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1736" class="line" lang="plaintext">l l l.</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1737
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1737" class="line" lang="plaintext">qmask:hardmask:action</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1738
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1738" class="line" lang="plaintext">_</span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="1739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1739
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1739" class="line" lang="plaintext">none:off:no masking, all symbols used, no change</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="1740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1740
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1740" class="line" lang="plaintext">none:on:no masking, all symbols used, no change</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1741
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1741" class="line" lang="plaintext">dust:off:masked symbols lowercased, rest uppercased</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1742
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1742" class="line" lang="plaintext">dust:on:masked symbols changed to Ns, rest unchanged</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1743
</td>
<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1743" class="line" lang="plaintext">soft:off:lowercase symbols masked, no case changes</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1744
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<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1744" class="line" lang="plaintext">soft:on:lowercase symbols masked and changed to Ns</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1745
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<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1745" class="line" lang="plaintext">.TE</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1746
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<td class="diff-line-num new_line old" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1746" class="line" lang="plaintext">.ce 0 \# end of centering</span>
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<td class="diff-line-num new old_line" data-linenumber="1747" style="width: 35px; color: rgba(0,0,0,0.3); 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="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1963
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<pre style="margin: 0;">+<span id="LC1963" class="line" lang="plaintext">.RE</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1747
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<td class="diff-line-num new_line" data-linenumber="1964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1964
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1964" class="line" lang="plaintext">.PP</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="1748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1965
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<pre style="margin: 0;">+<span id="LC1965" class="line" lang="plaintext">.RS</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="1748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1966
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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="LC1966" class="line" lang="plaintext">.TAG fastaout</span>
</pre>
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</tr>
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<td class="diff-line-num old_line" data-linenumber="1748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1748
</td>
<td class="diff-line-num new_line" data-linenumber="1967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1967
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1967" class="line" lang="plaintext">.TP 9</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="1749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1749
</td>
<td class="diff-line-num new_line" data-linenumber="1968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1968
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1968" class="line" lang="plaintext">.BI \-\-fastaout \0filename</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="1750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1750
</td>
<td class="diff-line-num new_line" data-linenumber="1969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1969
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1969" class="line" lang="plaintext">Write the masked sequences to \fIfilename\fR, in fasta format. Applies</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="1751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1751
</td>
<td class="diff-line-num new_line" data-linenumber="1970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1970
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1970" class="line" lang="plaintext">only to the \-\-fastx_mask command.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1971
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<pre style="margin: 0;">+<span id="LC1971" class="line" lang="plaintext">.TAG fastqout</span>
</pre>
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</tr>
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<td class="diff-line-num old_line" data-linenumber="1752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1752
</td>
<td class="diff-line-num new_line" data-linenumber="1972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1972
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1972" class="line" lang="plaintext">.TP</span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1753
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<td class="diff-line-num new_line" data-linenumber="1973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1973
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1973" class="line" lang="plaintext">.BI \-\-fastqout \0filename</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="1754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1754
</td>
<td class="diff-line-num new_line" data-linenumber="1974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1974
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1974" class="line" lang="plaintext">Write the masked sequences to \fIfilename\fR, in fastq format. Applies</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1755
</td>
<td class="diff-line-num new_line" data-linenumber="1975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1975
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1975" class="line" lang="plaintext">only to the \-\-fastx_mask command.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1976
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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="LC1976" class="line" lang="plaintext">.TAG fastx_mask</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1756
</td>
<td class="diff-line-num new_line" data-linenumber="1977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1977
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1977" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1757
</td>
<td class="diff-line-num new_line" data-linenumber="1978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1978
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1978" class="line" lang="plaintext">.BI \-\-fastx_mask \0filename</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1758
</td>
<td class="diff-line-num new_line" data-linenumber="1979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1979
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1979" class="line" lang="plaintext">Mask regions in sequences contained</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1762" style="width: 35px; color: rgba(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="1983" style="width: 35px; color: rgba(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">@@ -1762,10 +1983,12 @@ are specified with the \-\-fastaout and \-\-fastqout options. The</td>
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<td class="diff-line-num old_line" data-linenumber="1762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1762
</td>
<td class="diff-line-num new_line" data-linenumber="1983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1983
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1983" class="line" lang="plaintext">minimum and maximum percentage of unmasked residues may be specified</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1763
</td>
<td class="diff-line-num new_line" data-linenumber="1984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1984
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1984" class="line" lang="plaintext">with the \-\-min_unmasked_pct and \-\-max_unmasked_pct options,</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1764
</td>
<td class="diff-line-num new_line" data-linenumber="1985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1985
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1985" class="line" lang="plaintext">respectively.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1986
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1986" class="line" lang="plaintext">.TAG hardmask</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1765
</td>
<td class="diff-line-num new_line" data-linenumber="1987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1987
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1987" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1766
</td>
<td class="diff-line-num new_line" data-linenumber="1988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1988
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<pre style="margin: 0;"> <span id="LC1988" class="line" lang="plaintext">.B \-\-hardmask</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1767
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<td class="diff-line-num new_line" data-linenumber="1989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1989
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1989" class="line" lang="plaintext">Symbols in masked regions are replaced by N's. The default is to</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="1768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1768
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<td class="diff-line-num new_line" data-linenumber="1990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1990
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1990" class="line" lang="plaintext">replace the masked regions by lower case letters.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1991
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<pre style="margin: 0;">+<span id="LC1991" class="line" lang="plaintext">.TAG maskfasta</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1769
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<td class="diff-line-num new_line" data-linenumber="1992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1992
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1992" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1770
</td>
<td class="diff-line-num new_line" data-linenumber="1993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1993
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1993" class="line" lang="plaintext">.BI \-\-maskfasta \0filename</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="1771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1771
</td>
<td class="diff-line-num new_line" data-linenumber="1994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1994
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1994" class="line" lang="plaintext">Mask regions in sequences contained</span>
</pre>
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</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1773" style="width: 35px; color: rgba(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="1996" style="width: 35px; color: rgba(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">@@ -1773,18 +1996,22 @@ in the fasta file \fIfilename\fR. The default is to mask using</td>
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<td class="diff-line-num old_line" data-linenumber="1773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1773
</td>
<td class="diff-line-num new_line" data-linenumber="1996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1996
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1996" class="line" lang="plaintext">\fIdust\fR (use \-\-qmask to modify that behavior). The output file is</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="1774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1774
</td>
<td class="diff-line-num new_line" data-linenumber="1997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1997
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1997" class="line" lang="plaintext">specified with the \-\-output option. This command is depreciated,</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="1775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1775
</td>
<td class="diff-line-num new_line" data-linenumber="1998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1998
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1998" class="line" lang="plaintext">please use \-\-fastx_mask instead.</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="1776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1999
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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="LC1999" class="line" lang="plaintext">.TAG max_unmasked_pct</span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1776
</td>
<td class="diff-line-num new_line" data-linenumber="2000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2000
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2000" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1777
</td>
<td class="diff-line-num new_line" data-linenumber="2001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2001
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2001" class="line" lang="plaintext">.BI \-\-max_unmasked_pct \0real</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1778
</td>
<td class="diff-line-num new_line" data-linenumber="2002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2002
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2002" class="line" lang="plaintext">Discard sequences with more than the specified maximum percentage of</span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1779
</td>
<td class="diff-line-num new_line" data-linenumber="2003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2003
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2003" class="line" lang="plaintext">unmasked residues. Works only with \-\-fastx_mask.</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="1780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2004
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<pre style="margin: 0;">+<span id="LC2004" class="line" lang="plaintext">.TAG min_unmasked_pct</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1780
</td>
<td class="diff-line-num new_line" data-linenumber="2005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2005
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2005" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1781
</td>
<td class="diff-line-num new_line" data-linenumber="2006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2006
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2006" class="line" lang="plaintext">.BI \-\-min_unmasked_pct \0real</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1782
</td>
<td class="diff-line-num new_line" data-linenumber="2007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2007
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2007" class="line" lang="plaintext">Discard sequences with less than the specified minimum percentage of</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1783
</td>
<td class="diff-line-num new_line" data-linenumber="2008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2008
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2008" class="line" lang="plaintext">unmasked residues. Works only with \-\-fastx_mask.</span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2009
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2009" class="line" lang="plaintext">.TAG output</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1784
</td>
<td class="diff-line-num new_line" data-linenumber="2010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2010
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2010" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1785
</td>
<td class="diff-line-num new_line" data-linenumber="2011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2011
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2011" class="line" lang="plaintext">.BI \-\-output \0filename</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1786
</td>
<td class="diff-line-num new_line" data-linenumber="2012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2012
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2012" class="line" lang="plaintext">Write the masked sequences to \fIfilename\fR, in fasta format. Applies</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1787
</td>
<td class="diff-line-num new_line" data-linenumber="2013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2013
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2013" class="line" lang="plaintext">only to the \-\-mask_fasta command.</span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2014
</td>
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<pre style="margin: 0;">+<span id="LC2014" class="line" lang="plaintext">.TAG qmask</span>
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1788
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2015
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<pre style="margin: 0;"> <span id="LC2015" class="line" lang="plaintext">.TP</span>
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1789
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2016
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<pre style="margin: 0;"> <span id="LC2016" class="line" lang="plaintext">.BI \-\-qmask\~ "none|dust|soft"</span>
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1790
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2017
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<pre style="margin: 0;"> <span id="LC2017" class="line" lang="plaintext">If the argument is dust, mask regions in sequences using the</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1795" style="width: 35px; color: rgba(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="2022" style="width: 35px; color: rgba(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">@@ -1795,6 +2022,7 @@ mask.</td>
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1795
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2022
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<pre style="margin: 0;"> <span id="LC2022" class="line" lang="plaintext">.RE</span>
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1796
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2023
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<pre style="margin: 0;"> <span id="LC2023" class="line" lang="plaintext">.PP</span>
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1797
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2024
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<pre style="margin: 0;"> <span id="LC2024" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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2025
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<pre style="margin: 0;">+<span id="LC2025" class="line" lang="plaintext">.TAG restriction-site-cutting-options</span>
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1798
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2026
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<pre style="margin: 0;"> <span id="LC2026" class="line" lang="plaintext">Restriction site cutting options:</span>
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1799
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2027
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<pre style="margin: 0;"> <span id="LC2027" class="line" lang="plaintext">.RS</span>
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1800
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2028
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<pre style="margin: 0;"> <span id="LC2028" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1807" style="width: 35px; color: rgba(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="2035" style="width: 35px; color: rgba(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">@@ -1807,11 +2035,13 @@ the \-\-fastaout_rev option. Input sequences that do not match are</td>
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1807
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2035
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<pre style="margin: 0;"> <span id="LC2035" class="line" lang="plaintext">written to the file specified with the option \-\-fastaout_discarded,</span>
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1808
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2036
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<pre style="margin: 0;"> <span id="LC2036" class="line" lang="plaintext">and their reverse complement are also written to the file specfied</span>
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1809
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2037
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<pre style="margin: 0;"> <span id="LC2037" class="line" lang="plaintext">with the \-\-fastaout_discarded_rev option. The relabel options</span>
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1810
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<pre style="margin: 0;">-<span id="LC1810" class="line" lang="plaintext">(\-\-relabel, \-\-relabel_keep, \-\-relabel_md5, and \-\-relabel_sha1)</span>
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1811
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<pre style="margin: 0;">-<span id="LC1811" class="line" lang="plaintext">may be used to relabel the output sequences).</span>
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2038
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<pre style="margin: 0;">+<span id="LC2038" class="line" lang="plaintext">(\-\-relabel, \-\-relabel_self, \-\-relabel_keep, \-\-relabel_md5, and</span>
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2039
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<pre style="margin: 0;">+<span id="LC2039" class="line" lang="plaintext">\-\-relabel_sha1) may be used to relabel the output sequences).</span>
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2040
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<pre style="margin: 0;">+<span id="LC2040" class="line" lang="plaintext">.TAG cut</span>
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1812
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2041
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<pre style="margin: 0;"> <span id="LC2041" class="line" lang="plaintext">.TP 9</span>
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1813
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2042
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<pre style="margin: 0;"> <span id="LC2042" class="line" lang="plaintext">.BI \-\-cut \0filename</span>
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1814
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2043
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<pre style="margin: 0;"> <span id="LC2043" class="line" lang="plaintext">Specify the input file with sequences in FASTA format.</span>
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2044
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<pre style="margin: 0;">+<span id="LC2044" class="line" lang="plaintext">.TAG cut_pattern</span>
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1815
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2045
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<pre style="margin: 0;"> <span id="LC2045" class="line" lang="plaintext">.TP</span>
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1816
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2046
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<pre style="margin: 0;"> <span id="LC2046" class="line" lang="plaintext">.BI \-\-cut_pattern \0string</span>
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1817
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<td class="diff-line-num new_line" data-linenumber="2047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2047
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<pre style="margin: 0;"> <span id="LC2047" class="line" lang="plaintext">Specify the restriction site cutting pattern and positions. The</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1825" style="width: 35px; color: rgba(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="2055" style="width: 35px; color: rgba(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">@@ -1825,17 +2055,21 @@ pattern for the EcoRI restriction site. For such palindromic patterns</td>
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1825
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2055
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<pre style="margin: 0;"> <span id="LC2055" class="line" lang="plaintext">possible fragments on both strands. For non-palindromic sites, it may</span>
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<td class="diff-line-num old_line" data-linenumber="1826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1826
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<td class="diff-line-num new_line" data-linenumber="2056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2056
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<pre style="margin: 0;"> <span id="LC2056" class="line" lang="plaintext">be necessary to run the command also on the reverse complemented input</span>
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<td class="diff-line-num old_line" data-linenumber="1827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1827
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<td class="diff-line-num new_line" data-linenumber="2057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2057
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<pre style="margin: 0;"> <span id="LC2057" class="line" lang="plaintext">sequences. Exactly one cutting site on each strand must be indicated.</span>
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<td class="diff-line-num new old_line" data-linenumber="1828" style="width: 35px; color: rgba(0,0,0,0.3); 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="2058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2058
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<pre style="margin: 0;">+<span id="LC2058" class="line" lang="plaintext">.TAG fastaout</span>
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<td class="diff-line-num old_line" data-linenumber="1828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1828
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<td class="diff-line-num new_line" data-linenumber="2059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2059
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<pre style="margin: 0;"> <span id="LC2059" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1829
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<td class="diff-line-num new_line" data-linenumber="2060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2060
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<pre style="margin: 0;"> <span id="LC2060" class="line" lang="plaintext">.BI \-\-fastaout \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1830
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<td class="diff-line-num new_line" data-linenumber="2061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2061
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<pre style="margin: 0;"> <span id="LC2061" class="line" lang="plaintext">Specify the output file for the resulting fragments on the forward</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1831
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<td class="diff-line-num new_line" data-linenumber="2062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2062
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<pre style="margin: 0;"> <span id="LC2062" class="line" lang="plaintext">strand.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1832" style="width: 35px; color: rgba(0,0,0,0.3); 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="2063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2063
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<pre style="margin: 0;">+<span id="LC2063" class="line" lang="plaintext">.TAG fastaout_rev</span>
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<td class="diff-line-num old_line" data-linenumber="1832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1832
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<td class="diff-line-num new_line" data-linenumber="2064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2064
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<pre style="margin: 0;"> <span id="LC2064" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1833
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<td class="diff-line-num new_line" data-linenumber="2065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2065
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<pre style="margin: 0;"> <span id="LC2065" class="line" lang="plaintext">.BI \-\-fastaout_rev \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1834
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<td class="diff-line-num new_line" data-linenumber="2066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2066
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<pre style="margin: 0;"> <span id="LC2066" class="line" lang="plaintext">Specify the output file for the resulting fragments on the reverse</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1835
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<td class="diff-line-num new_line" data-linenumber="2067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2067
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<pre style="margin: 0;"> <span id="LC2067" class="line" lang="plaintext">strand.</span>
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2068
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<pre style="margin: 0;">+<span id="LC2068" class="line" lang="plaintext">.TAG fastaout_discarded</span>
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<td class="diff-line-num old_line" data-linenumber="1836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1836
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<td class="diff-line-num new_line" data-linenumber="2069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2069
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<pre style="margin: 0;"> <span id="LC2069" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1837
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<td class="diff-line-num new_line" data-linenumber="2070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2070
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<pre style="margin: 0;"> <span id="LC2070" class="line" lang="plaintext">.BI \-\-fastaout_discarded \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1838
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<td class="diff-line-num new_line" data-linenumber="2071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2071
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<pre style="margin: 0;"> <span id="LC2071" class="line" lang="plaintext">Specify the output file for the non-matching sequences.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2072
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<pre style="margin: 0;">+<span id="LC2072" class="line" lang="plaintext">.TAG fastaout_discarded_rev</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1839
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<td class="diff-line-num new_line" data-linenumber="2073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2073
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<pre style="margin: 0;"> <span id="LC2073" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1840
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<td class="diff-line-num new_line" data-linenumber="2074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2074
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<pre style="margin: 0;"> <span id="LC2074" class="line" lang="plaintext">.BI \-\-fastaout_discarded_rev \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1841
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<td class="diff-line-num new_line" data-linenumber="2075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2075
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<pre style="margin: 0;"> <span id="LC2075" class="line" lang="plaintext">Specify the output file for the non-matching seqeunces, reverse</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1843" style="width: 35px; color: rgba(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="2077" style="width: 35px; color: rgba(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">@@ -1843,6 +2077,7 @@ complemented.</td>
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<td class="diff-line-num old_line" data-linenumber="1843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1843
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2077
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<pre style="margin: 0;"> <span id="LC2077" class="line" lang="plaintext">.RE</span>
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<td class="diff-line-num old_line" data-linenumber="1844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1844
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<td class="diff-line-num new_line" data-linenumber="2078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2078
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<pre style="margin: 0;"> <span id="LC2078" class="line" lang="plaintext">.PP</span>
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1845
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<td class="diff-line-num new_line" data-linenumber="2079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2079
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<pre style="margin: 0;"> <span id="LC2079" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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<td class="diff-line-num new old_line" data-linenumber="1846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2080
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<pre style="margin: 0;">+<span id="LC2080" class="line" lang="plaintext">.TAG pairwise-alignment-options</span>
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<td class="diff-line-num old_line" data-linenumber="1846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1846
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<td class="diff-line-num new_line" data-linenumber="2081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2081
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<pre style="margin: 0;"> <span id="LC2081" class="line" lang="plaintext">Pairwise alignment options:</span>
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<td class="diff-line-num old_line" data-linenumber="1847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1847
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<td class="diff-line-num new_line" data-linenumber="2082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2082
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<pre style="margin: 0;"> <span id="LC2082" class="line" lang="plaintext">.RS</span>
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1848
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<td class="diff-line-num new_line" data-linenumber="2083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2083
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<pre style="margin: 0;"> <span id="LC2083" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1855" style="width: 35px; color: rgba(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="2090" style="width: 35px; color: rgba(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">@@ -1855,24 +2090,29 @@ identity level with \-\-id to discard weak alignments. Most other</td>
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1855
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<td class="diff-line-num new_line" data-linenumber="2090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2090
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<pre style="margin: 0;"> <span id="LC2090" class="line" lang="plaintext">accept/reject options (see Searching options below) may also be</span>
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<td class="diff-line-num old_line" data-linenumber="1856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1856
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<td class="diff-line-num new_line" data-linenumber="2091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2091
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<pre style="margin: 0;"> <span id="LC2091" class="line" lang="plaintext">used. Sequences are aligned on their \fIplus\fR strand only. Masking</span>
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<td class="diff-line-num old_line" data-linenumber="1857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1857
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<td class="diff-line-num new_line" data-linenumber="2092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2092
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<pre style="margin: 0;"> <span id="LC2092" class="line" lang="plaintext">is performed as usual and specified with \-\-qmask and \-\-hardmask.</span>
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<td class="diff-line-num new old_line" data-linenumber="1858" style="width: 35px; color: rgba(0,0,0,0.3); 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="2093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2093
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<pre style="margin: 0;">+<span id="LC2093" class="line" lang="plaintext">.TAG acceptall</span>
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<td class="diff-line-num old_line" data-linenumber="1858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1858
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<td class="diff-line-num new_line" data-linenumber="2094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2094
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<pre style="margin: 0;"> <span id="LC2094" class="line" lang="plaintext">.TP 9</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1859
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<td class="diff-line-num new_line" data-linenumber="2095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2095
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<pre style="margin: 0;"> <span id="LC2095" class="line" lang="plaintext">.B \-\-acceptall</span>
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<td class="diff-line-num old_line" data-linenumber="1860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1860
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<td class="diff-line-num new_line" data-linenumber="2096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2096
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<pre style="margin: 0;"> <span id="LC2096" class="line" lang="plaintext">Write the results of all alignments to output files. This option</span>
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<td class="diff-line-num old_line" data-linenumber="1861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1861
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<td class="diff-line-num new_line" data-linenumber="2097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2097
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<pre style="margin: 0;"> <span id="LC2097" class="line" lang="plaintext">overrides all other accept/reject options (including \-\-id).</span>
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<td class="diff-line-num new old_line" data-linenumber="1862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2098
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<pre style="margin: 0;">+<span id="LC2098" class="line" lang="plaintext">.TAG allpairs_global</span>
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<td class="diff-line-num old_line" data-linenumber="1862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1862
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<td class="diff-line-num new_line" data-linenumber="2099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2099
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<pre style="margin: 0;"> <span id="LC2099" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1863
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<td class="diff-line-num new_line" data-linenumber="2100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2100
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<pre style="margin: 0;"> <span id="LC2100" class="line" lang="plaintext">.BI \-\-allpairs_global \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1864
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<td class="diff-line-num new_line" data-linenumber="2101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2101
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<pre style="margin: 0;"> <span id="LC2101" class="line" lang="plaintext">Perform optimal global pairwise alignments of all vs. all fasta</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1865
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<td class="diff-line-num new_line" data-linenumber="2102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2102
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<pre style="margin: 0;"> <span id="LC2102" class="line" lang="plaintext">sequences contained in \fIfilename\fR. This command is multi-threaded.</span>
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<td class="diff-line-num new old_line" data-linenumber="1866" style="width: 35px; color: rgba(0,0,0,0.3); 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="2103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2103
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<pre style="margin: 0;">+<span id="LC2103" class="line" lang="plaintext">.TAG id</span>
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1866
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<td class="diff-line-num new_line" data-linenumber="2104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2104
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<pre style="margin: 0;"> <span id="LC2104" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1867
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<td class="diff-line-num new_line" data-linenumber="2105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2105
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<pre style="margin: 0;"> <span id="LC2105" class="line" lang="plaintext">.BI \-\-id \0real</span>
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<td class="diff-line-num old_line" data-linenumber="1868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1868
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<td class="diff-line-num new_line" data-linenumber="2106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2106
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2106" class="line" lang="plaintext">Reject the sequence match if the pairwise identity is lower than</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1869
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<td class="diff-line-num new_line" data-linenumber="2107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2107
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<pre style="margin: 0;"> <span id="LC2107" class="line" lang="plaintext">\fIreal\fR (value ranging from 0.0 to 1.0 included).</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1870" style="width: 35px; color: rgba(0,0,0,0.3); 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="2108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2108
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<pre style="margin: 0;">+<span id="LC2108" class="line" lang="plaintext">.TAG threads</span>
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<td class="diff-line-num old_line" data-linenumber="1870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1870
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<td class="diff-line-num new_line" data-linenumber="2109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2109
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<pre style="margin: 0;"> <span id="LC2109" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1871
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<td class="diff-line-num new_line" data-linenumber="2110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2110
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<pre style="margin: 0;"> <span id="LC2110" class="line" lang="plaintext">.BI \-\-threads\~ "positive integer"</span>
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<td class="diff-line-num old_line" data-linenumber="1872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1872
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<td class="diff-line-num new_line" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2111
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<pre style="margin: 0;"> <span id="LC2111" class="line" lang="plaintext">Number of computation threads to use (1 to 1024). The number of</span>
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<td class="diff-line-num old_line" data-linenumber="1873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1873
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2112
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<pre style="margin: 0;"> <span id="LC2112" class="line" lang="plaintext">threads should be lesser or equal to the number of available CPU</span>
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1874
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<td class="diff-line-num new_line" data-linenumber="2113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2113
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<pre style="margin: 0;"> <span id="LC2113" class="line" lang="plaintext">cores. The default is to use all available resources and to launch one</span>
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1875
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2114
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<pre style="margin: 0;"> <span id="LC2114" class="line" lang="plaintext">thread per logical core.</span>
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<td class="diff-line-num new new_line" data-linenumber="2115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2115
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<pre style="margin: 0;">+<span id="LC2115" class="line" lang="plaintext">.TAG uc</span>
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<td class="diff-line-num old_line" data-linenumber="1876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1876
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<td class="diff-line-num new_line" data-linenumber="2116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2116
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<pre style="margin: 0;"> <span id="LC2116" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="1877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1877
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<td class="diff-line-num new_line" data-linenumber="2117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2117
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<pre style="margin: 0;"> <span id="LC2117" class="line" lang="plaintext">.BI \-\-uc \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="1878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1878
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<td class="diff-line-num new_line" data-linenumber="2118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2118
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<pre style="margin: 0;"> <span id="LC2118" class="line" lang="plaintext">Output pairwise alignment results in \fIfilename\fR using a</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1912" style="width: 35px; color: rgba(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="2152" style="width: 35px; color: rgba(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">@@ -1912,13 +2152,16 @@ Label of the target sequence.</td>
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<td class="diff-line-num old_line" data-linenumber="1912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1912
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<td class="diff-line-num new_line" data-linenumber="2152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2152
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<pre style="margin: 0;"> <span id="LC2152" class="line" lang="plaintext">.RE</span>
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<td class="diff-line-num old_line" data-linenumber="1913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1913
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<td class="diff-line-num new_line" data-linenumber="2153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2153
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<pre style="margin: 0;"> <span id="LC2153" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1914
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<td class="diff-line-num new_line" data-linenumber="2154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2154
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<pre style="margin: 0;"> <span id="LC2154" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1915" style="width: 35px; color: rgba(0,0,0,0.3); 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="2155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2155
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<pre style="margin: 0;">+<span id="LC2155" class="line" lang="plaintext">.TAG searching-options</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1915
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2156
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<pre style="margin: 0;"> <span id="LC2156" class="line" lang="plaintext">Searching options:</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1916
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<td class="diff-line-num new_line" data-linenumber="2157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2157
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<pre style="margin: 0;"> <span id="LC2157" class="line" lang="plaintext">.RS</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2158
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<pre style="margin: 0;">+<span id="LC2158" class="line" lang="plaintext">.TAG alnout</span>
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<td class="diff-line-num old_line" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1917
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2159
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<pre style="margin: 0;"> <span id="LC2159" class="line" lang="plaintext">.TP 9</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1918
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2160
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<pre style="margin: 0;"> <span id="LC2160" class="line" lang="plaintext">.BI \-\-alnout \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1919
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<td class="diff-line-num new_line" data-linenumber="2161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2161
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<pre style="margin: 0;"> <span id="LC2161" class="line" lang="plaintext">Write pairwise global alignments to \fIfilename\fR using a</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1920
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<td class="diff-line-num new_line" data-linenumber="2162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2162
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<pre style="margin: 0;"> <span id="LC2162" class="line" lang="plaintext">human-readable format. Use \-\-rowlen to modify alignment</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1921
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<td class="diff-line-num new_line" data-linenumber="2163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2163
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<pre style="margin: 0;"> <span id="LC2163" class="line" lang="plaintext">length. Output order may vary when using multiple threads.</span>
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<td class="diff-line-num new old_line" data-linenumber="1922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2164
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<pre style="margin: 0;">+<span id="LC2164" class="line" lang="plaintext">.TAG biomout</span>
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<td class="diff-line-num old_line" data-linenumber="1922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1922
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<td class="diff-line-num new_line" data-linenumber="2165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2165
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<pre style="margin: 0;"> <span id="LC2165" class="line" lang="plaintext">.TP</span>
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1923
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2166
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<pre style="margin: 0;"> <span id="LC2166" class="line" lang="plaintext">.BI \-\-biomout \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1924
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2167
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<pre style="margin: 0;"> <span id="LC2167" class="line" lang="plaintext">Write search results to an OTU table in the biom version 1.0 file</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1926" style="width: 35px; color: rgba(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="2169" style="width: 35px; color: rgba(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">@@ -1926,6 +2169,7 @@ format. The query file contains the samples, while the database file</td>
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<td class="diff-line-num old_line" data-linenumber="1926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1926
</td>
<td class="diff-line-num new_line" data-linenumber="2169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2169
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2169" class="line" lang="plaintext">contains the OTUs. Sample and OTU identifiers are extracted from the</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1927
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<td class="diff-line-num new_line" data-linenumber="2170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2170
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2170" class="line" lang="plaintext">header of these sequences. See the \-\-biomout option in the</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1928
</td>
<td class="diff-line-num new_line" data-linenumber="2171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2171
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2171" class="line" lang="plaintext">Clustering section for further details.</span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2172
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<pre style="margin: 0;">+<span id="LC2172" class="line" lang="plaintext">.TAG blast6out</span>
</pre>
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</tr>
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<td class="diff-line-num old_line" data-linenumber="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1929
</td>
<td class="diff-line-num new_line" data-linenumber="2173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2173
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2173" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1930
</td>
<td class="diff-line-num new_line" data-linenumber="2174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2174
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2174" class="line" lang="plaintext">.BI \-\-blast6out \0filename</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="1931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1931
</td>
<td class="diff-line-num new_line" data-linenumber="2175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2175
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2175" class="line" lang="plaintext">Write search results to \fIfilename\fR using a blast-like</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1986" style="width: 35px; color: rgba(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="2230" style="width: 35px; color: rgba(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">@@ -1986,6 +2230,7 @@ alignments). Always set to -1.</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1986
</td>
<td class="diff-line-num new_line" data-linenumber="2230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2230
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2230" class="line" lang="plaintext">alignments). Always set to 0.</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1987
</td>
<td class="diff-line-num new_line" data-linenumber="2231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2231
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2231" class="line" lang="plaintext">.RE</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1988
</td>
<td class="diff-line-num new_line" data-linenumber="2232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2232
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2232" class="line" lang="plaintext">.RE</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2233
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2233" class="line" lang="plaintext">.TAG db</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1989
</td>
<td class="diff-line-num new_line" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2234
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2234" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1990
</td>
<td class="diff-line-num new_line" data-linenumber="2235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2235
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2235" class="line" lang="plaintext">.BI \-\-db \0filename</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1991
</td>
<td class="diff-line-num new_line" data-linenumber="2236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2236
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2236" class="line" lang="plaintext">Compare query sequences (specified with \-\-usearch_global) to the</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1993" style="width: 35px; color: rgba(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="2238" style="width: 35px; color: rgba(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">@@ -1993,32 +2238,38 @@ fasta-formatted target sequences contained in \fIfilename\fR, using</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1993
</td>
<td class="diff-line-num new_line" data-linenumber="2238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2238
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2238" class="line" lang="plaintext">global pairwise alignment. Alternatively, the name of a preformatted</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1994
</td>
<td class="diff-line-num new_line" data-linenumber="2239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2239
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2239" class="line" lang="plaintext">UDB database created using the makeudb_usearch command (see below) may</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1995
</td>
<td class="diff-line-num new_line" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2240
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2240" class="line" lang="plaintext">be specified.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2241
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2241" class="line" lang="plaintext">.TAG dbmask</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1996
</td>
<td class="diff-line-num new_line" data-linenumber="2242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2242
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2242" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1997
</td>
<td class="diff-line-num new_line" data-linenumber="2243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2243
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2243" class="line" lang="plaintext">.BI \-\-dbmask\~ "none|dust|soft"</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1998
</td>
<td class="diff-line-num new_line" data-linenumber="2244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2244
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2244" class="line" lang="plaintext">Mask regions in the target database sequences using the dust method or</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1999
</td>
<td class="diff-line-num new_line" data-linenumber="2245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2245
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2245" class="line" lang="plaintext">the soft method, or do not mask (none). Warning, when using soft</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2000
</td>
<td class="diff-line-num new_line" data-linenumber="2246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2246
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2246" class="line" lang="plaintext">masking search commands become case sensitive. The default is to mask</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2001
</td>
<td class="diff-line-num new_line" data-linenumber="2247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2247
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2247" class="line" lang="plaintext">using dust.</span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="2002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2248
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<pre style="margin: 0;">+<span id="LC2248" class="line" lang="plaintext">.TAG dbmatched</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2002
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<td class="diff-line-num new_line" data-linenumber="2249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2249
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2249" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2003
</td>
<td class="diff-line-num new_line" data-linenumber="2250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2250
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2250" class="line" lang="plaintext">.BI \-\-dbmatched \0filename</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="2004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2004
</td>
<td class="diff-line-num new_line" data-linenumber="2251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2251
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2251" class="line" lang="plaintext">Write database target sequences matching at least one query sequence</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="2005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2005
</td>
<td class="diff-line-num new_line" data-linenumber="2252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2252
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2252" class="line" lang="plaintext">to \fIfilename\fR, in fasta format. If the option \-\-sizeout is used,</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2006
</td>
<td class="diff-line-num new_line" data-linenumber="2253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2253
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2253" class="line" lang="plaintext">the number of queries that matched each target sequence is indicated</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2007
</td>
<td class="diff-line-num new_line" data-linenumber="2254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2254
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2254" class="line" lang="plaintext">using the pattern ";size=\fIinteger\fR;".</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="2008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2255
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2255" class="line" lang="plaintext">.TAG dbnotmatched</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2008
</td>
<td class="diff-line-num new_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2256
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2256" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2009
</td>
<td class="diff-line-num new_line" data-linenumber="2257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2257
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2257" class="line" lang="plaintext">.BI \-\-dbnotmatched \0filename</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2010
</td>
<td class="diff-line-num new_line" data-linenumber="2258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2258
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2258" class="line" lang="plaintext">Write database target sequences not matching query sequences to</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2011
</td>
<td class="diff-line-num new_line" data-linenumber="2259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2259
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2259" class="line" lang="plaintext">\fIfilename\fR, in fasta format.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2260
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2260" class="line" lang="plaintext">.TAG fastapairs</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2012
</td>
<td class="diff-line-num new_line" data-linenumber="2261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2261
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2261" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2013
</td>
<td class="diff-line-num new_line" data-linenumber="2262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2262
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2262" class="line" lang="plaintext">.BI \-\-fastapairs \0filename</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2014
</td>
<td class="diff-line-num new_line" data-linenumber="2263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2263
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2263" class="line" lang="plaintext">Write pairwise alignments of query and target sequences to</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2015
</td>
<td class="diff-line-num new_line" data-linenumber="2264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2264
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2264" class="line" lang="plaintext">\fIfilename\fR, in fasta format.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2265
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2265" class="line" lang="plaintext">.TAG fulldp</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2016
</td>
<td class="diff-line-num new_line" data-linenumber="2266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2266
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2266" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2017
</td>
<td class="diff-line-num new_line" data-linenumber="2267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2267
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2267" class="line" lang="plaintext">.B \-\-fulldp</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2018
</td>
<td class="diff-line-num new_line" data-linenumber="2268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2268
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2268" class="line" lang="plaintext">Dummy option for compatibility with usearch. To maximize search</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2019
</td>
<td class="diff-line-num new_line" data-linenumber="2269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2269
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2269" class="line" lang="plaintext">sensitivity, \fBvsearch\fR uses a 8-way 16-bit SIMD vectorized full</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2020
</td>
<td class="diff-line-num new_line" data-linenumber="2270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2270
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2270" class="line" lang="plaintext">dynamic programming algorithm (Needleman-Wunsch), whether or not</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2021
</td>
<td class="diff-line-num new_line" data-linenumber="2271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2271
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2271" class="line" lang="plaintext">\-\-fulldp is specified.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2272
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2272" class="line" lang="plaintext">.TAG gapext</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2022
</td>
<td class="diff-line-num new_line" data-linenumber="2273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2273
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2273" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2023
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<td class="diff-line-num new_line" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2274
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<pre style="margin: 0;"> <span id="LC2274" class="line" lang="plaintext">.BI \-\-gapext \0string</span>
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<td class="diff-line-num old_line" data-linenumber="2024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2024
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<td class="diff-line-num new_line" data-linenumber="2275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2275
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<pre style="margin: 0;"> <span id="LC2275" class="line" lang="plaintext">Set penalties for a gap extension. See \-\-gapopen for a complete</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2026" style="width: 35px; color: rgba(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="2277" style="width: 35px; color: rgba(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">@@ -2026,6 +2277,7 @@ description of the penalty declaration system. The default is to</td>
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2026
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2277
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<pre style="margin: 0;"> <span id="LC2277" class="line" lang="plaintext">initialize the six gap extending penalties using a penalty of 2 for</span>
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<td class="diff-line-num old_line" data-linenumber="2027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2027
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<td class="diff-line-num new_line" data-linenumber="2278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2278
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<pre style="margin: 0;"> <span id="LC2278" class="line" lang="plaintext">extending internal gaps and a penalty of 1 for extending terminal</span>
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<td class="diff-line-num old_line" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2028
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<td class="diff-line-num new_line" data-linenumber="2279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2279
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<pre style="margin: 0;"> <span id="LC2279" class="line" lang="plaintext">gaps, in both query and target sequences (i.e. 2I/1E).</span>
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<td class="diff-line-num new old_line" data-linenumber="2029" style="width: 35px; color: rgba(0,0,0,0.3); 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="2280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2280
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<pre style="margin: 0;">+<span id="LC2280" class="line" lang="plaintext">.TAG gapopen</span>
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2029
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<td class="diff-line-num new_line" data-linenumber="2281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2281
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<pre style="margin: 0;"> <span id="LC2281" class="line" lang="plaintext">.TP</span>
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2030
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<td class="diff-line-num new_line" data-linenumber="2282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2282
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<pre style="margin: 0;"> <span id="LC2282" class="line" lang="plaintext">.BI \-\-gapopen \0string</span>
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<td class="diff-line-num old_line" data-linenumber="2031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2031
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<td class="diff-line-num new_line" data-linenumber="2283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2283
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<pre style="margin: 0;"> <span id="LC2283" class="line" lang="plaintext">Set penalties for a gap opening. A gap opening can occur in six</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2060" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2060,11 +2312,13 @@ integer gap penalties. Because the lowest gap penalties are 0.5 by</td>
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2060
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2312
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<pre style="margin: 0;"> <span id="LC2312" class="line" lang="plaintext">default in usearch, all default scores and gap penalties in</span>
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<td class="diff-line-num old_line" data-linenumber="2061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2061
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC2313" class="line" lang="plaintext">\fBvsearch\fR have been doubled to maintain equivalent penalties and</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2062
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<td class="diff-line-num new_line" data-linenumber="2314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2314
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<pre style="margin: 0;"> <span id="LC2314" class="line" lang="plaintext">to produce identical alignments.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2063" style="width: 35px; color: rgba(0,0,0,0.3); 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="2315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2315
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<pre style="margin: 0;">+<span id="LC2315" class="line" lang="plaintext">.TAG hardmask</span>
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<td class="diff-line-num old_line" data-linenumber="2063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2063
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC2316" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2064
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<td class="diff-line-num new_line" data-linenumber="2317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2317
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<pre style="margin: 0;"> <span id="LC2317" class="line" lang="plaintext">.B \-\-hardmask</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2065
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<td class="diff-line-num new_line" data-linenumber="2318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2318
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<pre style="margin: 0;"> <span id="LC2318" class="line" lang="plaintext">Mask sequence regions by replacing them with Ns instead of setting</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2066
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<td class="diff-line-num 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">
2319
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<pre style="margin: 0;"> <span id="LC2319" class="line" lang="plaintext">them to lower case as is the default. For more information, please see</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2067
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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="plaintext">the Masking section.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2068" style="width: 35px; color: rgba(0,0,0,0.3); 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="2321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2321
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<pre style="margin: 0;">+<span id="LC2321" class="line" lang="plaintext">.TAG id</span>
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2068
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<td class="diff-line-num new_line" data-linenumber="2322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2322
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<pre style="margin: 0;"> <span id="LC2322" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2069
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<td class="diff-line-num new_line" data-linenumber="2323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2323
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<pre style="margin: 0;"> <span id="LC2323" class="line" lang="plaintext">.BI \-\-id \0real</span>
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<td class="diff-line-num old_line" data-linenumber="2070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2070
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<td class="diff-line-num new_line" data-linenumber="2324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2324
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2324" class="line" lang="plaintext">Reject the sequence match if the pairwise identity is lower than</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2080" style="width: 35px; color: rgba(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="2334" style="width: 35px; color: rgba(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">@@ -2080,6 +2334,7 @@ query needs to match the target. Consequently, using values lower than</td>
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2080
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<td class="diff-line-num new_line" data-linenumber="2334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2334
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<pre style="margin: 0;"> <span id="LC2334" class="line" lang="plaintext">pairwise identity is by default defined as the number of (matching</span>
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2081
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<td class="diff-line-num new_line" data-linenumber="2335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2335
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<pre style="margin: 0;"> <span id="LC2335" class="line" lang="plaintext">columns) / (alignment length - terminal gaps). That definition can be</span>
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2082
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<td class="diff-line-num new_line" data-linenumber="2336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2336
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<pre style="margin: 0;"> <span id="LC2336" class="line" lang="plaintext">modified by \-\-iddef.</span>
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<td class="diff-line-num new new_line" data-linenumber="2337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2337
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<pre style="margin: 0;">+<span id="LC2337" class="line" lang="plaintext">.TAG iddef</span>
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2083
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<td class="diff-line-num new_line" data-linenumber="2338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2338
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<pre style="margin: 0;"> <span id="LC2338" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="2084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2084
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<td class="diff-line-num new_line" data-linenumber="2339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2339
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<pre style="margin: 0;"> <span id="LC2339" class="line" lang="plaintext">.BI \-\-iddef\~ "0|1|2|3|4"</span>
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<td class="diff-line-num old_line" data-linenumber="2085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2085
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<td class="diff-line-num new_line" data-linenumber="2340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2340
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<pre style="margin: 0;"> <span id="LC2340" class="line" lang="plaintext">Change the pairwise identity definition used in \-\-id. Values</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2107" style="width: 35px; color: rgba(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="2362" style="width: 35px; color: rgba(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">@@ -2107,25 +2362,31 @@ The option \-\-userfields accepts the fields id0 to id4, in addition</td>
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<td class="diff-line-num old_line" data-linenumber="2107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2107
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<td class="diff-line-num new_line" data-linenumber="2362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2362
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<pre style="margin: 0;"> <span id="LC2362" class="line" lang="plaintext">to the field id, to report the pairwise identity values corresponding</span>
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<td class="diff-line-num old_line" data-linenumber="2108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2108
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<td class="diff-line-num new_line" data-linenumber="2363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2363
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<pre style="margin: 0;"> <span id="LC2363" class="line" lang="plaintext">to the different definitions.</span>
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<td class="diff-line-num old_line" data-linenumber="2109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2109
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<td class="diff-line-num new_line" data-linenumber="2364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2364
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<pre style="margin: 0;"> <span id="LC2364" class="line" lang="plaintext">.RE</span>
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<td class="diff-line-num new old_line" data-linenumber="2110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2365
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<pre style="margin: 0;">+<span id="LC2365" class="line" lang="plaintext">.TAG idprefix</span>
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<td class="diff-line-num old_line" data-linenumber="2110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2110
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<td class="diff-line-num new_line" data-linenumber="2366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2366
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<pre style="margin: 0;"> <span id="LC2366" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2111
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<td class="diff-line-num new_line" data-linenumber="2367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2367
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<pre style="margin: 0;"> <span id="LC2367" class="line" lang="plaintext">.BI \-\-idprefix\~ "positive integer"</span>
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<td class="diff-line-num old_line" data-linenumber="2112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2112
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<td class="diff-line-num new_line" data-linenumber="2368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2368
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<pre style="margin: 0;"> <span id="LC2368" class="line" lang="plaintext">Reject the sequence match if the first \fIinteger\fR nucleotides of</span>
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<td class="diff-line-num old_line" data-linenumber="2113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2113
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<td class="diff-line-num new_line" data-linenumber="2369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2369
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<pre style="margin: 0;"> <span id="LC2369" class="line" lang="plaintext">the target do not match the query.</span>
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<td class="diff-line-num new old_line" data-linenumber="2114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2370
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<pre style="margin: 0;">+<span id="LC2370" class="line" lang="plaintext">.TAG idsuffix</span>
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<td class="diff-line-num old_line" data-linenumber="2114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2114
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<td class="diff-line-num new_line" data-linenumber="2371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2371
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<pre style="margin: 0;"> <span id="LC2371" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2115
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<td class="diff-line-num new_line" data-linenumber="2372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2372
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<pre style="margin: 0;"> <span id="LC2372" class="line" lang="plaintext">.BI \-\-idsuffix\~ "positive integer"</span>
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<td class="diff-line-num old_line" data-linenumber="2116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2116
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<td class="diff-line-num new_line" data-linenumber="2373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2373
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<pre style="margin: 0;"> <span id="LC2373" class="line" lang="plaintext">Reject the sequence match if the last \fIinteger\fR nucleotides of the</span>
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<td class="diff-line-num old_line" data-linenumber="2117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2117
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<td class="diff-line-num new_line" data-linenumber="2374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2374
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<pre style="margin: 0;"> <span id="LC2374" class="line" lang="plaintext">target do not match the query.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2375
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<pre style="margin: 0;">+<span id="LC2375" class="line" lang="plaintext">.TAG leftjust</span>
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<td class="diff-line-num old_line" data-linenumber="2118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2118
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<td class="diff-line-num new_line" data-linenumber="2376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2376
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<pre style="margin: 0;"> <span id="LC2376" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2119
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<td class="diff-line-num new_line" data-linenumber="2377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2377
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<pre style="margin: 0;"> <span id="LC2377" class="line" lang="plaintext">.B \-\-leftjust</span>
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<td class="diff-line-num old_line" data-linenumber="2120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2120
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<td class="diff-line-num new_line" data-linenumber="2378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2378
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2378" class="line" lang="plaintext">Reject the sequence match if the pairwise alignment begins with gaps.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2379
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<pre style="margin: 0;">+<span id="LC2379" class="line" lang="plaintext">.TAG match</span>
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<td class="diff-line-num old_line" data-linenumber="2121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2121
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<td class="diff-line-num new_line" data-linenumber="2380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2380
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2380" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2122
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<td class="diff-line-num new_line" data-linenumber="2381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2381
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<pre style="margin: 0;"> <span id="LC2381" class="line" lang="plaintext">.BI \-\-match\~ "integer"</span>
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2123
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<td class="diff-line-num new_line" data-linenumber="2382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2382
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<pre style="margin: 0;"> <span id="LC2382" class="line" lang="plaintext">Score assigned to a match (i.e. identical nucleotides) in the pairwise</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2124
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<td class="diff-line-num new_line" data-linenumber="2383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2383
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<pre style="margin: 0;"> <span id="LC2383" class="line" lang="plaintext">alignment. The default value is 2.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2125" style="width: 35px; color: rgba(0,0,0,0.3); 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="2384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2384
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<pre style="margin: 0;">+<span id="LC2384" class="line" lang="plaintext">.TAG matched</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2125
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<td class="diff-line-num new_line" data-linenumber="2385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2385
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<pre style="margin: 0;"> <span id="LC2385" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2126
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<td class="diff-line-num new_line" data-linenumber="2386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2386
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2386" class="line" lang="plaintext">.BI \-\-matched \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2127
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<td class="diff-line-num new_line" data-linenumber="2387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2387
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2387" class="line" lang="plaintext">Write query sequences matching database target sequences to</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2128
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<td class="diff-line-num new_line" data-linenumber="2388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2388
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<pre style="margin: 0;"> <span id="LC2388" class="line" lang="plaintext">\fIfilename\fR, in fasta format.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2389
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<pre style="margin: 0;">+<span id="LC2389" class="line" lang="plaintext">.TAG maxaccepts</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2129
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<td class="diff-line-num new_line" data-linenumber="2390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2390
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<pre style="margin: 0;"> <span id="LC2390" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2130
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<td class="diff-line-num new_line" data-linenumber="2391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2391
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<pre style="margin: 0;"> <span id="LC2391" class="line" lang="plaintext">.BI \-\-maxaccepts\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2131
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<td class="diff-line-num new_line" data-linenumber="2392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2392
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2392" class="line" lang="plaintext">Maximum number of hits to accept before stopping the search. The</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2138" style="width: 35px; color: rgba(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="2399" style="width: 35px; color: rgba(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">@@ -2138,31 +2399,38 @@ criteria, it is accepted as best hit and the search process stops for</td>
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<td class="diff-line-num old_line" data-linenumber="2138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2138
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<td class="diff-line-num new_line" data-linenumber="2399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2399
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2399" class="line" lang="plaintext">that query. If \-\-maxaccepts is set to a higher value, more hits are</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2139
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<td class="diff-line-num new_line" data-linenumber="2400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2400
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2400" class="line" lang="plaintext">accepted. If \-\-maxaccepts and \-\-maxrejects are both set to 0, the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2140
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<td class="diff-line-num new_line" data-linenumber="2401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2401
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2401" class="line" lang="plaintext">complete database is searched.</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="2141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2402
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<pre style="margin: 0;">+<span id="LC2402" class="line" lang="plaintext">.TAG maxdiffs</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2141
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<td class="diff-line-num new_line" data-linenumber="2403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2403
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2403" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2142
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<td class="diff-line-num new_line" data-linenumber="2404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2404
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2404" class="line" lang="plaintext">.BI \-\-maxdiffs\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2143
</td>
<td class="diff-line-num new_line" data-linenumber="2405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2405
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2405" class="line" lang="plaintext">Reject the sequence match if the alignment contains at least</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2144
</td>
<td class="diff-line-num new_line" data-linenumber="2406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2406
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2406" class="line" lang="plaintext">\fIinteger\fR substitutions, insertions or deletions.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2407
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<pre style="margin: 0;">+<span id="LC2407" class="line" lang="plaintext">.TAG maxgaps</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2145
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<td class="diff-line-num new_line" data-linenumber="2408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2408
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2408" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2146
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<td class="diff-line-num new_line" data-linenumber="2409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2409
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2409" class="line" lang="plaintext">.BI \-\-maxgaps\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2147
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<td class="diff-line-num new_line" data-linenumber="2410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2410
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2410" class="line" lang="plaintext">Reject the sequence match if the alignment contains at least</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2148
</td>
<td class="diff-line-num new_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">
2411
</td>
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<pre style="margin: 0;"> <span id="LC2411" class="line" lang="plaintext">\fIinteger\fR insertions or deletions.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2412
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<pre style="margin: 0;">+<span id="LC2412" class="line" lang="plaintext">.TAG maxhits</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2149
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<td class="diff-line-num new_line" data-linenumber="2413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2413
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<pre style="margin: 0;"> <span id="LC2413" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2150
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<td class="diff-line-num new_line" data-linenumber="2414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2414
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<pre style="margin: 0;"> <span id="LC2414" class="line" lang="plaintext">.BI \-\-maxhits\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2151
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<td class="diff-line-num new_line" data-linenumber="2415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2415
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<pre style="margin: 0;"> <span id="LC2415" class="line" lang="plaintext">Maximum number of hits to show once the search is terminated (hits are</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2152
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<td class="diff-line-num new_line" data-linenumber="2416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2416
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<pre style="margin: 0;"> <span id="LC2416" class="line" lang="plaintext">sorted by decreasing identity). Unlimited by default. That option</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2153
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<td class="diff-line-num new_line" data-linenumber="2417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2417
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<pre style="margin: 0;"> <span id="LC2417" class="line" lang="plaintext">applies to \-\-alnout, \-\-blast6out, \-\-fastapairs, \-\-samout,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2154
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<td class="diff-line-num new_line" data-linenumber="2418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2418
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<pre style="margin: 0;"> <span id="LC2418" class="line" lang="plaintext">\-\-uc, or \-\-userout output files.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2155" style="width: 35px; color: rgba(0,0,0,0.3); 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="2419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2419
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<pre style="margin: 0;">+<span id="LC2419" class="line" lang="plaintext">.TAG maxid</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2155
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<td class="diff-line-num new_line" data-linenumber="2420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2420
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<pre style="margin: 0;"> <span id="LC2420" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2156
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<td class="diff-line-num new_line" data-linenumber="2421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2421
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<pre style="margin: 0;"> <span id="LC2421" class="line" lang="plaintext">.BI \-\-maxid \0real</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2157
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<td class="diff-line-num new_line" data-linenumber="2422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2422
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<pre style="margin: 0;"> <span id="LC2422" class="line" lang="plaintext">Reject the sequence match if the percentage of identity between the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2158
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<td class="diff-line-num new_line" data-linenumber="2423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2423
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<pre style="margin: 0;"> <span id="LC2423" class="line" lang="plaintext">two sequences is greater than \fIreal\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2424
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<pre style="margin: 0;">+<span id="LC2424" class="line" lang="plaintext">.TAG maxqsize</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2159
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<td class="diff-line-num new_line" data-linenumber="2425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2425
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<pre style="margin: 0;"> <span id="LC2425" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2160
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<td class="diff-line-num new_line" data-linenumber="2426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2426
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<pre style="margin: 0;"> <span id="LC2426" class="line" lang="plaintext">.BI \-\-maxqsize\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2161
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<td class="diff-line-num new_line" data-linenumber="2427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2427
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2427" class="line" lang="plaintext">Reject query sequences with an abundance greater than \fIinteger\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2428
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<pre style="margin: 0;">+<span id="LC2428" class="line" lang="plaintext">.TAG maxqt</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2162
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<td class="diff-line-num new_line" data-linenumber="2429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2429
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<pre style="margin: 0;"> <span id="LC2429" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2163
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<td class="diff-line-num new_line" data-linenumber="2430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2430
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<pre style="margin: 0;"> <span id="LC2430" class="line" lang="plaintext">.BI \-\-maxqt \0real</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2164
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<td class="diff-line-num new_line" data-linenumber="2431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2431
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<pre style="margin: 0;"> <span id="LC2431" class="line" lang="plaintext">Reject if the query/target sequence length ratio is greater than</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2165
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<td class="diff-line-num new_line" data-linenumber="2432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2432
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2432" class="line" lang="plaintext">\fIreal\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2433
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<pre style="margin: 0;">+<span id="LC2433" class="line" lang="plaintext">.TAG maxrejects</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2166
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<td class="diff-line-num new_line" data-linenumber="2434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2434
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2434" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2167
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<td class="diff-line-num new_line" data-linenumber="2435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2435
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2435" class="line" lang="plaintext">.BI \-\-maxrejects\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2168
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<td class="diff-line-num new_line" data-linenumber="2436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2436
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2436" class="line" lang="plaintext">Maximum number of non-matching target sequences to consider before</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2176" style="width: 35px; color: rgba(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="2444" style="width: 35px; color: rgba(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">@@ -2176,40 +2444,50 @@ process stops for that query (no hit). If \-\-maxrejects is set to a</td>
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<td class="diff-line-num old_line" data-linenumber="2176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2176
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<td class="diff-line-num new_line" data-linenumber="2444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2444
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2444" class="line" lang="plaintext">higher value, more target sequences are considered. If \-\-maxaccepts</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2177
</td>
<td class="diff-line-num new_line" data-linenumber="2445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2445
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<pre style="margin: 0;"> <span id="LC2445" class="line" lang="plaintext">and \-\-maxrejects are both set to 0, the complete database is</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2178
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<td class="diff-line-num new_line" data-linenumber="2446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2446
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<pre style="margin: 0;"> <span id="LC2446" class="line" lang="plaintext">searched.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2179" style="width: 35px; color: rgba(0,0,0,0.3); 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="2447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2447
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<pre style="margin: 0;">+<span id="LC2447" class="line" lang="plaintext">.TAG maxsizeratio</span>
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<td class="diff-line-num old_line" data-linenumber="2179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2179
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<td class="diff-line-num new_line" data-linenumber="2448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2448
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<pre style="margin: 0;"> <span id="LC2448" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2180
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<td class="diff-line-num new_line" data-linenumber="2449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2449
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<pre style="margin: 0;"> <span id="LC2449" class="line" lang="plaintext">.BI \-\-maxsizeratio \0real</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2181
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<td class="diff-line-num new_line" data-linenumber="2450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2450
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<pre style="margin: 0;"> <span id="LC2450" class="line" lang="plaintext">Reject if the query/target abundance ratio is greater than</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2182
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<td class="diff-line-num new_line" data-linenumber="2451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2451
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<pre style="margin: 0;"> <span id="LC2451" class="line" lang="plaintext">\fIreal\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2452
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<pre style="margin: 0;">+<span id="LC2452" class="line" lang="plaintext">.TAG maxsl</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2183
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<td class="diff-line-num new_line" data-linenumber="2453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2453
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<pre style="margin: 0;"> <span id="LC2453" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2184
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<td class="diff-line-num new_line" data-linenumber="2454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2454
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<pre style="margin: 0;"> <span id="LC2454" class="line" lang="plaintext">.BI \-\-maxsl \0real</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2185
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<td class="diff-line-num new_line" data-linenumber="2455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2455
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2455" class="line" lang="plaintext">Reject if the shorter/longer sequence length ratio is</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2186
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<td class="diff-line-num new_line" data-linenumber="2456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2456
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2456" class="line" lang="plaintext">greater than \fIreal\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2457
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<pre style="margin: 0;">+<span id="LC2457" class="line" lang="plaintext">.TAG maxsubs</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2187
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<td class="diff-line-num new_line" data-linenumber="2458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2458
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2458" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2188
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<td class="diff-line-num new_line" data-linenumber="2459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2459
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2459" class="line" lang="plaintext">.BI \-\-maxsubs\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2189
</td>
<td class="diff-line-num new_line" data-linenumber="2460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2460
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2460" class="line" lang="plaintext">Reject the sequence match if the pairwise alignment contains more than</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2190
</td>
<td class="diff-line-num new_line" data-linenumber="2461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2461
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2461" class="line" lang="plaintext">\fIinteger\fR substitutions.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2462
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<pre style="margin: 0;">+<span id="LC2462" class="line" lang="plaintext">.TAG mid</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2191
</td>
<td class="diff-line-num new_line" data-linenumber="2463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2463
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2463" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2192
</td>
<td class="diff-line-num new_line" data-linenumber="2464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2464
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2464" class="line" lang="plaintext">.BI \-\-mid \0real</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2193
</td>
<td class="diff-line-num new_line" data-linenumber="2465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2465
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2465" class="line" lang="plaintext">Reject the sequence match if the percentage of identity is lower than</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="2194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2194
</td>
<td class="diff-line-num new_line" data-linenumber="2466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2466
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2466" class="line" lang="plaintext">\fIreal\fR (ignoring all gaps, internal and terminal).</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2467
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<pre style="margin: 0;">+<span id="LC2467" class="line" lang="plaintext">.TAG mincols</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2195
</td>
<td class="diff-line-num new_line" data-linenumber="2468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2468
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2468" class="line" lang="plaintext">.TP</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="2196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2196
</td>
<td class="diff-line-num new_line" data-linenumber="2469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2469
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2469" class="line" lang="plaintext">.BI \-\-mincols\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2197
</td>
<td class="diff-line-num new_line" data-linenumber="2470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2470
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2470" class="line" lang="plaintext">Reject the sequence match if the alignment length is shorter than</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2198
</td>
<td class="diff-line-num new_line" data-linenumber="2471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2471
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2471" class="line" lang="plaintext">\fIinteger\fR.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2472
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<pre style="margin: 0;">+<span id="LC2472" class="line" lang="plaintext">.TAG minqt</span>
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<td class="diff-line-num old_line" data-linenumber="2199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2199
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<td class="diff-line-num new_line" data-linenumber="2473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2473
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<pre style="margin: 0;"> <span id="LC2473" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2200
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<td class="diff-line-num new_line" data-linenumber="2474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2474
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<pre style="margin: 0;"> <span id="LC2474" class="line" lang="plaintext">.BI \-\-minqt \0real</span>
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<td class="diff-line-num old_line" data-linenumber="2201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2201
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<td class="diff-line-num new_line" data-linenumber="2475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2475
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<pre style="margin: 0;"> <span id="LC2475" class="line" lang="plaintext">Reject if the query/target sequence length ratio is lower than</span>
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<td class="diff-line-num old_line" data-linenumber="2202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2202
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<td class="diff-line-num new_line" data-linenumber="2476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2476
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<pre style="margin: 0;"> <span id="LC2476" class="line" lang="plaintext">\fIreal\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2203" style="width: 35px; color: rgba(0,0,0,0.3); 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="2477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2477
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<pre style="margin: 0;">+<span id="LC2477" class="line" lang="plaintext">.TAG minsizeratio</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2203
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<td class="diff-line-num new_line" data-linenumber="2478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2478
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<pre style="margin: 0;"> <span id="LC2478" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2204
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<td class="diff-line-num new_line" data-linenumber="2479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2479
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<pre style="margin: 0;"> <span id="LC2479" class="line" lang="plaintext">.BI \-\-minsizeratio \0real</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2205
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<td class="diff-line-num new_line" data-linenumber="2480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2480
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2480" class="line" lang="plaintext">Reject if the query/target abundance ratio is lower than \fIreal\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2206" style="width: 35px; color: rgba(0,0,0,0.3); 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="2481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2481
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<pre style="margin: 0;">+<span id="LC2481" class="line" lang="plaintext">.TAG minsl</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2206
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<td class="diff-line-num new_line" data-linenumber="2482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2482
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<pre style="margin: 0;"> <span id="LC2482" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2207
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<td class="diff-line-num new_line" data-linenumber="2483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2483
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<pre style="margin: 0;"> <span id="LC2483" class="line" lang="plaintext">.BI \-\-minsl \0real</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2208
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<td class="diff-line-num new_line" data-linenumber="2484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2484
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2484" class="line" lang="plaintext">Reject if the shorter/longer sequence length ratio is lower than</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2209
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<td class="diff-line-num new_line" data-linenumber="2485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2485
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<pre style="margin: 0;"> <span id="LC2485" class="line" lang="plaintext">\fIreal\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2210" style="width: 35px; color: rgba(0,0,0,0.3); 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="2486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2486
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<pre style="margin: 0;">+<span id="LC2486" class="line" lang="plaintext">.TAG mintsize</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2210
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<td class="diff-line-num new_line" data-linenumber="2487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2487
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2487" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2211
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<td class="diff-line-num new_line" data-linenumber="2488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2488
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<pre style="margin: 0;"> <span id="LC2488" class="line" lang="plaintext">.BI \-\-mintsize\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2212
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<td class="diff-line-num new_line" data-linenumber="2489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2489
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2489" class="line" lang="plaintext">Reject target sequences with an abundance lower than \fIinteger\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2213" style="width: 35px; color: rgba(0,0,0,0.3); 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="2490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2490
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<pre style="margin: 0;">+<span id="LC2490" class="line" lang="plaintext">.TAG minwordmatches</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2213
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<td class="diff-line-num new_line" data-linenumber="2491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2491
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<pre style="margin: 0;"> <span id="LC2491" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2214
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<td class="diff-line-num new_line" data-linenumber="2492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2492
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<pre style="margin: 0;"> <span id="LC2492" class="line" lang="plaintext">.BI \-\-minwordmatches\~ "non-negative integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2215
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<td class="diff-line-num new_line" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2493
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2493" class="line" lang="plaintext">Minimum number of word matches required for a sequence to be</span>
</pre>
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</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2219" style="width: 35px; color: rgba(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="2497" style="width: 35px; color: rgba(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">@@ -2219,10 +2497,12 @@ considered further. Default value is 12 for the default word length</td>
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<td class="diff-line-num old_line" data-linenumber="2219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2219
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<td class="diff-line-num new_line" data-linenumber="2497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2497
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<pre style="margin: 0;"> <span id="LC2497" class="line" lang="plaintext">sequence has fewer unique words than the number specified, all words</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2220
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<td class="diff-line-num new_line" data-linenumber="2498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2498
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2498" class="line" lang="plaintext">in the query must match. If the argument is 0, no word matches are</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2221
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<td class="diff-line-num new_line" data-linenumber="2499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2499
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<pre style="margin: 0;"> <span id="LC2499" class="line" lang="plaintext">required.</span>
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2500
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<pre style="margin: 0;">+<span id="LC2500" class="line" lang="plaintext">.TAG mismatch</span>
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2222
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2501
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<pre style="margin: 0;"> <span id="LC2501" class="line" lang="plaintext">.TP</span>
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2223
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2502
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<pre style="margin: 0;"> <span id="LC2502" class="line" lang="plaintext">.BI \-\-mismatch\~ "integer"</span>
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2224
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<td class="diff-line-num new_line" data-linenumber="2503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2503
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<pre style="margin: 0;"> <span id="LC2503" class="line" lang="plaintext">Score assigned to a mismatch (i.e. different nucleotides) in the</span>
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<td class="diff-line-num old_line" data-linenumber="2225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2225
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<td class="diff-line-num new_line" data-linenumber="2504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2504
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<pre style="margin: 0;"> <span id="LC2504" class="line" lang="plaintext">pairwise alignment. The default value is -4.</span>
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<td class="diff-line-num new new_line" data-linenumber="2505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2505
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<pre style="margin: 0;">+<span id="LC2505" class="line" lang="plaintext">.TAG mothur_shared_out</span>
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<td class="diff-line-num old_line" data-linenumber="2226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2226
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<td class="diff-line-num new_line" data-linenumber="2506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2506
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<pre style="margin: 0;"> <span id="LC2506" class="line" lang="plaintext">.TP</span>
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2227
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<td class="diff-line-num new_line" data-linenumber="2507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2507
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<pre style="margin: 0;"> <span id="LC2507" class="line" lang="plaintext">.BI \-\-mothur_shared_out \0filename</span>
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2228
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<td class="diff-line-num new_line" data-linenumber="2508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2508
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<pre style="margin: 0;"> <span id="LC2508" class="line" lang="plaintext">Write search results to an OTU table in the mothur 'shared'</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2230" style="width: 35px; color: rgba(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="2510" style="width: 35px; color: rgba(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">@@ -2230,10 +2510,12 @@ tab-separated plain text file format. The query file contains the</td>
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2230
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<td class="diff-line-num new_line" data-linenumber="2510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2510
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<pre style="margin: 0;"> <span id="LC2510" class="line" lang="plaintext">samples, while the database file contains the OTUs. Sample and OTU</span>
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<td class="diff-line-num old_line" data-linenumber="2231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2231
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<td class="diff-line-num new_line" data-linenumber="2511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2511
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<pre style="margin: 0;"> <span id="LC2511" class="line" lang="plaintext">identifiers are extracted from the header of these sequences. See the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2232
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<td class="diff-line-num new_line" data-linenumber="2512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2512
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<pre style="margin: 0;"> <span id="LC2512" class="line" lang="plaintext">\-\-otutabout option in the Clustering section for further details.</span>
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2513
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<pre style="margin: 0;">+<span id="LC2513" class="line" lang="plaintext">.TAG notmatched</span>
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<td class="diff-line-num old_line" data-linenumber="2233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2233
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<td class="diff-line-num new_line" data-linenumber="2514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2514
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2514" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2234
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<td class="diff-line-num new_line" data-linenumber="2515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2515
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<pre style="margin: 0;"> <span id="LC2515" class="line" lang="plaintext">.BI \-\-notmatched \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="2235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2235
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<td class="diff-line-num new_line" data-linenumber="2516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2516
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<pre style="margin: 0;"> <span id="LC2516" class="line" lang="plaintext">Write query sequences not matching database target sequences to</span>
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<td class="diff-line-num old_line" data-linenumber="2236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2236
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<td class="diff-line-num new_line" data-linenumber="2517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2517
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<pre style="margin: 0;"> <span id="LC2517" class="line" lang="plaintext">\fIfilename\fR, in fasta format.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2237" style="width: 35px; color: rgba(0,0,0,0.3); 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="2518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2518
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<pre style="margin: 0;">+<span id="LC2518" class="line" lang="plaintext">.TAG otutabout</span>
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<td class="diff-line-num old_line" data-linenumber="2237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2237
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<td class="diff-line-num new_line" data-linenumber="2519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2519
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<pre style="margin: 0;"> <span id="LC2519" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="2238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2238
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<td class="diff-line-num new_line" data-linenumber="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2520
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<pre style="margin: 0;"> <span id="LC2520" class="line" lang="plaintext">.BI \-\-otutabout \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2239
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<td class="diff-line-num new_line" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2521
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2521" class="line" lang="plaintext">Write search results to an OTU table in the classic tab-separated</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2242" style="width: 35px; color: rgba(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="2524" style="width: 35px; color: rgba(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">@@ -2242,39 +2524,49 @@ database file contains the OTUs. Sample and OTU identifiers are</td>
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<td class="diff-line-num old_line" data-linenumber="2242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2242
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<td class="diff-line-num new_line" data-linenumber="2524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2524
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2524" class="line" lang="plaintext">extracted from the header of these sequences. See the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2243
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<td class="diff-line-num new_line" data-linenumber="2525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2525
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2525" class="line" lang="plaintext">\-\-mothur_shared_out option in the Clustering section for further</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2244
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<td class="diff-line-num new_line" data-linenumber="2526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2526
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2526" class="line" lang="plaintext">details.</span>
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<td class="diff-line-num new old_line" data-linenumber="2245" style="width: 35px; color: rgba(0,0,0,0.3); 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="2527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2527
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<pre style="margin: 0;">+<span id="LC2527" class="line" lang="plaintext">.TAG output_no_hits</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2245
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<td class="diff-line-num new_line" data-linenumber="2528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2528
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<pre style="margin: 0;"> <span id="LC2528" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2246
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<td class="diff-line-num new_line" data-linenumber="2529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2529
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<pre style="margin: 0;"> <span id="LC2529" class="line" lang="plaintext">.B \-\-output_no_hits</span>
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<td class="diff-line-num old_line" data-linenumber="2247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2247
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<td class="diff-line-num new_line" data-linenumber="2530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2530
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<pre style="margin: 0;"> <span id="LC2530" class="line" lang="plaintext">Write both matching and non-matching queries to \-\-alnout,</span>
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<td class="diff-line-num old_line" data-linenumber="2248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2248
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<td class="diff-line-num new_line" data-linenumber="2531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2531
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<pre style="margin: 0;"> <span id="LC2531" class="line" lang="plaintext">\-\-blast6out, \-\-samout or \-\-userout output files. Non-matching</span>
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<td class="diff-line-num old_line" data-linenumber="2249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2249
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<td class="diff-line-num new_line" data-linenumber="2532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2532
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<pre style="margin: 0;"> <span id="LC2532" class="line" lang="plaintext">queries are labelled 'No hits' in \-\-alnout files.</span>
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<td class="diff-line-num new old_line" data-linenumber="2250" style="width: 35px; color: rgba(0,0,0,0.3); 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="2533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2533
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<pre style="margin: 0;">+<span id="LC2533" class="line" lang="plaintext">.TAG pattern</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2250
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<td class="diff-line-num new_line" data-linenumber="2534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2534
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<pre style="margin: 0;"> <span id="LC2534" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2251
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<td class="diff-line-num new_line" data-linenumber="2535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2535
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<pre style="margin: 0;"> <span id="LC2535" class="line" lang="plaintext">.B \-\-pattern \fIstring\fR</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2252
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<td class="diff-line-num new_line" data-linenumber="2536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2536
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<pre style="margin: 0;"> <span id="LC2536" class="line" lang="plaintext">This option is ignored. It is provided for compatibility with usearch.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2537
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<pre style="margin: 0;">+<span id="LC2537" class="line" lang="plaintext">.TAG qmask</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2253
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<td class="diff-line-num new_line" data-linenumber="2538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2538
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<pre style="margin: 0;"> <span id="LC2538" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2254
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<td class="diff-line-num new_line" data-linenumber="2539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2539
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<pre style="margin: 0;"> <span id="LC2539" class="line" lang="plaintext">.BI \-\-qmask\~ "none|dust|soft"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2255
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<td class="diff-line-num new_line" data-linenumber="2540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2540
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2540" class="line" lang="plaintext">Mask regions in the query sequences</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2256
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<td class="diff-line-num new_line" data-linenumber="2541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2541
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<pre style="margin: 0;"> <span id="LC2541" class="line" lang="plaintext">using the dust or the soft algorithms, or do not mask</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2257
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<td class="diff-line-num new_line" data-linenumber="2542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2542
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<pre style="margin: 0;"> <span id="LC2542" class="line" lang="plaintext">(none). Warning, when using soft masking search commands</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2258
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<td class="diff-line-num new_line" data-linenumber="2543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2543
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<pre style="margin: 0;"> <span id="LC2543" class="line" lang="plaintext">become case sensitive. The default is to mask using \fIdust\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2259" style="width: 35px; color: rgba(0,0,0,0.3); 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="2544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2544
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<pre style="margin: 0;">+<span id="LC2544" class="line" lang="plaintext">.TAG query_cov</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2259
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<td class="diff-line-num new_line" data-linenumber="2545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2545
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<pre style="margin: 0;"> <span id="LC2545" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2260
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<td class="diff-line-num new_line" data-linenumber="2546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2546
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<pre style="margin: 0;"> <span id="LC2546" class="line" lang="plaintext">.BI \-\-query_cov \0real</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2261
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<td class="diff-line-num new_line" data-linenumber="2547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2547
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2547" class="line" lang="plaintext">Reject if the fraction of the query aligned to the target sequence is</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2262
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<td class="diff-line-num new_line" data-linenumber="2548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2548
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2548" class="line" lang="plaintext">lower than \fIreal\fR. The query coverage is computed as</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2263
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<td class="diff-line-num new_line" data-linenumber="2549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2549
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2549" class="line" lang="plaintext">(matches + mismatches) / query sequence length. Internal or terminal</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2264
</td>
<td class="diff-line-num new_line" data-linenumber="2550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2550
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<pre style="margin: 0;"> <span id="LC2550" class="line" lang="plaintext">gaps are not taken into account.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2265" style="width: 35px; color: rgba(0,0,0,0.3); 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="2551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2551
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<pre style="margin: 0;">+<span id="LC2551" class="line" lang="plaintext">.TAG rightjust</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2265
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<td class="diff-line-num new_line" data-linenumber="2552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2552
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2552" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2266
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2553
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<pre style="margin: 0;"> <span id="LC2553" class="line" lang="plaintext">.B \-\-rightjust</span>
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2267
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2554
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<pre style="margin: 0;"> <span id="LC2554" class="line" lang="plaintext">Reject the sequence match if the pairwise alignment ends with gaps.</span>
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<td class="diff-line-num new old_line" data-linenumber="2268" style="width: 35px; color: rgba(0,0,0,0.3); 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="2555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2555
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<pre style="margin: 0;">+<span id="LC2555" class="line" lang="plaintext">.TAG rowlen</span>
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2268
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2556
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<pre style="margin: 0;"> <span id="LC2556" class="line" lang="plaintext">.TP</span>
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2269
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2557
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<pre style="margin: 0;"> <span id="LC2557" class="line" lang="plaintext">.BI \-\-rowlen\~ "positive integer"</span>
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2270
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2558
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<pre style="margin: 0;"> <span id="LC2558" class="line" lang="plaintext">Width of alignment lines in \-\-alnout output. The default value is</span>
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2271
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<td class="diff-line-num new_line" data-linenumber="2559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2559
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<pre style="margin: 0;"> <span id="LC2559" class="line" lang="plaintext">64. Set to 0 to eliminate wrapping.</span>
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2560
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<pre style="margin: 0;">+<span id="LC2560" class="line" lang="plaintext">.TAG samheader</span>
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2272
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2561
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<pre style="margin: 0;"> <span id="LC2561" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="2273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2273
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2562
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<pre style="margin: 0;"> <span id="LC2562" class="line" lang="plaintext">.B \-\-samheader</span>
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<td class="diff-line-num old_line" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2274
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<td class="diff-line-num new_line" data-linenumber="2563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2563
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<pre style="margin: 0;"> <span id="LC2563" class="line" lang="plaintext">Include header lines to the SAM file when \-\-samout is specified. The</span>
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<td class="diff-line-num old_line" data-linenumber="2275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2275
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<td class="diff-line-num new_line" data-linenumber="2564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2564
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<pre style="margin: 0;"> <span id="LC2564" class="line" lang="plaintext">header includes lines starting with @HD, @SQ and @PG, but no @RG lines</span>
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2276
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<td class="diff-line-num new_line old" data-linenumber="2565" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2276" class="line" lang="plaintext">(see <https://github.com/samtools/hts-specs>). By default no header</span>
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<td class="diff-line-num old old_line" data-linenumber="2277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2277
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<td class="diff-line-num new_line old" data-linenumber="2565" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2277" class="line" lang="plaintext">line is written.</span>
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<td class="diff-line-num new old_line" data-linenumber="2278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2565
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<pre style="margin: 0;">+<span id="LC2565" class="line" lang="plaintext">(see</span>
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2566
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<pre style="margin: 0;">+<span id="LC2566" class="line" lang="plaintext">.URL https://github.com/samtools/hts-specs (link)</span>
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2567
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<pre style="margin: 0;">+<span id="LC2567" class="line" lang="plaintext"><https://github.com/samtools/hts-specs>). By default no header line is</span>
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2568
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<pre style="margin: 0;">+<span id="LC2568" class="line" lang="plaintext">written.</span>
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2569
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<pre style="margin: 0;">+<span id="LC2569" class="line" lang="plaintext">.TAG samout</span>
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2278
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2570
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<pre style="margin: 0;"> <span id="LC2570" class="line" lang="plaintext">.TP</span>
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2279
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2571
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<pre style="margin: 0;"> <span id="LC2571" class="line" lang="plaintext">.BI \-\-samout \0filename</span>
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2280
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2572
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<pre style="margin: 0;"> <span id="LC2572" class="line" lang="plaintext">Write alignment results to \fIfilename\fR using the SAM format (a</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2283" style="width: 35px; color: rgba(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="2575" style="width: 35px; color: rgba(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">@@ -2283,8 +2575,10 @@ file starts with header lines. Each non-header line is a SAM record,</td>
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2283
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2575
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<pre style="margin: 0;"> <span id="LC2575" class="line" lang="plaintext">which represents either a query-target alignment or the absence of</span>
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<td class="diff-line-num old_line" data-linenumber="2284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2284
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<td class="diff-line-num new_line" data-linenumber="2576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2576
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<pre style="margin: 0;"> <span id="LC2576" class="line" lang="plaintext">match for a query (output order may vary when using multiple</span>
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<td class="diff-line-num old_line" data-linenumber="2285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2285
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<td class="diff-line-num new_line" data-linenumber="2577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2577
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<pre style="margin: 0;"> <span id="LC2577" class="line" lang="plaintext">threads). Each record contains 11 mandatory fields and optional fields</span>
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2286
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<pre style="margin: 0;">-<span id="LC2286" class="line" lang="plaintext">(see <https://github.com/samtools/hts-specs> for a complete</span>
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<td class="diff-line-num old old_line" data-linenumber="2287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2287
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<td class="diff-line-num new_line old" data-linenumber="2578" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2287" class="line" lang="plaintext">description of the format):</span>
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2578
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<pre style="margin: 0;">+<span id="LC2578" class="line" lang="plaintext">(see</span>
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2579
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<pre style="margin: 0;">+<span id="LC2579" class="line" lang="plaintext">.URL https://github.com/samtools/hts-specs (link)</span>
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2580
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<pre style="margin: 0;">+<span id="LC2580" class="line" lang="plaintext"><https://github.com/samtools/hts-specs> for a complete description of</span>
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<td class="diff-line-num new new_line" data-linenumber="2581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2581
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<pre style="margin: 0;">+<span id="LC2581" class="line" lang="plaintext">the format):</span>
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2288
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2582
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<pre style="margin: 0;"> <span id="LC2582" class="line" lang="plaintext">.RS</span>
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2289
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2583
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<pre style="margin: 0;"> <span id="LC2583" class="line" lang="plaintext">.RS</span>
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2290
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2584
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<pre style="margin: 0;"> <span id="LC2584" class="line" lang="plaintext">.nr step 1 1</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2318" style="width: 35px; color: rgba(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="2612" style="width: 35px; color: rgba(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">@@ -2318,9 +2612,7 @@ as usearch does).</td>
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2318
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2612
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<pre style="margin: 0;"> <span id="LC2612" class="line" lang="plaintext">.IP \n+[step].</span>
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<td class="diff-line-num old_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">
2319
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2613
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<pre style="margin: 0;"> <span id="LC2613" class="line" lang="plaintext">quality string (ignored, always set to '*').</span>
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2320
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2614
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<pre style="margin: 0;"> <span id="LC2614" class="line" lang="plaintext">.RE</span>
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2321
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<pre style="margin: 0;">-<span id="LC2321" class="line" lang="plaintext">.TP</span>
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2322
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<pre style="margin: 0;">-<span id="LC2322" class="line" lang="plaintext">Optional fields for query-target matches (number and order of fields</span>
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2323
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<pre style="margin: 0;">-<span id="LC2323" class="line" lang="plaintext">may vary):</span>
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2615
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<pre style="margin: 0;">+<span id="LC2615" class="line" lang="plaintext">Optional fields for query-target matches (number and order of fields may vary):</span>
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2324
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<td class="diff-line-num new_line" data-linenumber="2616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2616
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<pre style="margin: 0;"> <span id="LC2616" class="line" lang="plaintext">.RS</span>
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<td class="diff-line-num old_line" data-linenumber="2325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2325
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2617
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<pre style="margin: 0;"> <span id="LC2617" class="line" lang="plaintext">.nr step 12 1</span>
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2326
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2618
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<pre style="margin: 0;"> <span id="LC2618" class="line" lang="plaintext">.IP \n[step]. 4</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2633" style="width: 35px; color: rgba(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">@@ -2341,6 +2633,7 @@ MD:Z:? string for mismatching positions.</td>
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2341
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2633
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<pre style="margin: 0;"> <span id="LC2633" class="line" lang="plaintext">YT:Z:UU string representing the alignment type.</span>
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2342
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2634
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<pre style="margin: 0;"> <span id="LC2634" class="line" lang="plaintext">.RE</span>
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2343
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2635
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<pre style="margin: 0;"> <span id="LC2635" class="line" lang="plaintext">.RE</span>
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2636
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<pre style="margin: 0;">+<span id="LC2636" class="line" lang="plaintext">.TAG search_exact</span>
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2344
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<td class="diff-line-num new_line" data-linenumber="2637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2637
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<pre style="margin: 0;"> <span id="LC2637" class="line" lang="plaintext">.TP</span>
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2345
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2638
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<pre style="margin: 0;"> <span id="LC2638" class="line" lang="plaintext">.BI \-\-search_exact \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="2346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2346
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<td class="diff-line-num new_line" data-linenumber="2639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2639
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<pre style="margin: 0;"> <span id="LC2639" class="line" lang="plaintext">Search for exact full-length matches to the query sequences contained</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2642" style="width: 35px; color: rgba(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">@@ -2349,29 +2642,35 @@ in \fIfilename\fR in the database of target sequences (\-\-db). Only</td>
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<td class="diff-line-num old_line" data-linenumber="2349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2349
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<td class="diff-line-num new_line" data-linenumber="2642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2642
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<pre style="margin: 0;"> <span id="LC2642" class="line" lang="plaintext">\-\-usearch_global. The \-\-id, \-\-maxaccepts and \-\-maxrejects</span>
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<td class="diff-line-num old_line" data-linenumber="2350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2350
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<td class="diff-line-num new_line" data-linenumber="2643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2643
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<pre style="margin: 0;"> <span id="LC2643" class="line" lang="plaintext">options are ignored, but the rest of the searching options may be</span>
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<td class="diff-line-num old_line" data-linenumber="2351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2351
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<td class="diff-line-num new_line" data-linenumber="2644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2644
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<pre style="margin: 0;"> <span id="LC2644" class="line" lang="plaintext">specified.</span>
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<td class="diff-line-num new old_line" data-linenumber="2352" style="width: 35px; color: rgba(0,0,0,0.3); 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="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2645
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<pre style="margin: 0;">+<span id="LC2645" class="line" lang="plaintext">.TAG self</span>
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<td class="diff-line-num old_line" data-linenumber="2352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2352
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<td class="diff-line-num new_line" data-linenumber="2646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2646
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<pre style="margin: 0;"> <span id="LC2646" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2353
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<td class="diff-line-num new_line" data-linenumber="2647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2647
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<pre style="margin: 0;"> <span id="LC2647" class="line" lang="plaintext">.B \-\-self</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2354
</td>
<td class="diff-line-num new_line" data-linenumber="2648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2648
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<pre style="margin: 0;"> <span id="LC2648" class="line" lang="plaintext">Reject the sequence match if the query and target labels are</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2355
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<td class="diff-line-num new_line" data-linenumber="2649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2649
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<pre style="margin: 0;"> <span id="LC2649" class="line" lang="plaintext">identical.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2356" style="width: 35px; color: rgba(0,0,0,0.3); 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="2650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2650
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<pre style="margin: 0;">+<span id="LC2650" class="line" lang="plaintext">.TAG selfid</span>
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<td class="diff-line-num old_line" data-linenumber="2356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2356
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<td class="diff-line-num new_line" data-linenumber="2651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2651
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<pre style="margin: 0;"> <span id="LC2651" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2357
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<td class="diff-line-num new_line" data-linenumber="2652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2652
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<pre style="margin: 0;"> <span id="LC2652" class="line" lang="plaintext">.B \-\-selfid</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2358
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<td class="diff-line-num new_line" data-linenumber="2653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2653
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<pre style="margin: 0;"> <span id="LC2653" class="line" lang="plaintext">Reject the sequence match if the query and target sequences are</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2359
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<td class="diff-line-num new_line" data-linenumber="2654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2654
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<pre style="margin: 0;"> <span id="LC2654" class="line" lang="plaintext">strictly identical.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2360" style="width: 35px; color: rgba(0,0,0,0.3); 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="2655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2655
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<pre style="margin: 0;">+<span id="LC2655" class="line" lang="plaintext">.TAG sizeout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2360
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<td class="diff-line-num new_line" data-linenumber="2656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2656
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<pre style="margin: 0;"> <span id="LC2656" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2361
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<td class="diff-line-num new_line" data-linenumber="2657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2657
</td>
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<pre style="margin: 0;"> <span id="LC2657" class="line" lang="plaintext">.B \-\-sizeout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2362
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<td class="diff-line-num new_line" data-linenumber="2658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2658
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<pre style="margin: 0;"> <span id="LC2658" class="line" lang="plaintext">Add abundance annotations to the output of the option \-\-dbmatched</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2363
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<td class="diff-line-num new_line" data-linenumber="2659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2659
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2659" class="line" lang="plaintext">(using the pattern ';size=\fIinteger\fR;'), to report the number of</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2364
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<td class="diff-line-num new_line" data-linenumber="2660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2660
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2660" class="line" lang="plaintext">queries that matched each target.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2661
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<pre style="margin: 0;">+<span id="LC2661" class="line" lang="plaintext">.TAG strand</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2365
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<td class="diff-line-num new_line" data-linenumber="2662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2662
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2662" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2366
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<td class="diff-line-num new_line" data-linenumber="2663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2663
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<pre style="margin: 0;"> <span id="LC2663" class="line" lang="plaintext">.BI \-\-strand\~ "plus|both"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2367
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<td class="diff-line-num new_line" data-linenumber="2664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2664
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2664" class="line" lang="plaintext">When searching for similar sequences, check the \fIplus\fR strand only</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2368
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<td class="diff-line-num new_line" data-linenumber="2665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2665
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2665" class="line" lang="plaintext">(default) or check \fIboth\fR strands.</span>
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2666
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<pre style="margin: 0;">+<span id="LC2666" class="line" lang="plaintext">.TAG target_cov</span>
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2369
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2667
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<pre style="margin: 0;"> <span id="LC2667" class="line" lang="plaintext">.TP</span>
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2370
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2668
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<pre style="margin: 0;"> <span id="LC2668" class="line" lang="plaintext">.BI \-\-target_cov \0real</span>
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<td class="diff-line-num old_line" data-linenumber="2371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2371
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<td class="diff-line-num new_line" data-linenumber="2669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2669
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<pre style="margin: 0;"> <span id="LC2669" class="line" lang="plaintext">Reject the sequence match if the fraction of the target sequence</span>
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2372
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<td class="diff-line-num new_line" data-linenumber="2670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2670
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<pre style="margin: 0;"> <span id="LC2670" class="line" lang="plaintext">aligned to the query sequence is lower than \fIreal\fR. The target</span>
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<td class="diff-line-num old_line" data-linenumber="2373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2373
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<td class="diff-line-num new_line" data-linenumber="2671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2671
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<pre style="margin: 0;"> <span id="LC2671" class="line" lang="plaintext">coverage is computed as (matches + mismatches) / target sequence</span>
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<td class="diff-line-num old_line" data-linenumber="2374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2374
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2672
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<pre style="margin: 0;"> <span id="LC2672" class="line" lang="plaintext">length. Internal or terminal gaps are not taken into account.</span>
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2673
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<pre style="margin: 0;">+<span id="LC2673" class="line" lang="plaintext">.TAG top_hits_only</span>
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2375
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2674
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<pre style="margin: 0;"> <span id="LC2674" class="line" lang="plaintext">.TP</span>
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2376
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2675
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<pre style="margin: 0;"> <span id="LC2675" class="line" lang="plaintext">.B \-\-top_hits_only</span>
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<td class="diff-line-num old_line" data-linenumber="2377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2377
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<td class="diff-line-num new_line" data-linenumber="2676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2676
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<pre style="margin: 0;"> <span id="LC2676" class="line" lang="plaintext">Only the top hits between the query and database sequence sets are</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2383" style="width: 35px; color: rgba(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="2682" style="width: 35px; color: rgba(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">@@ -2383,6 +2682,7 @@ the highest percentage of identity (see the \-\-iddef option to change</td>
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2383
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2682
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<pre style="margin: 0;"> <span id="LC2682" class="line" lang="plaintext">the way identity is measured). For a given query, if several top hits</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2384
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2683
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<pre style="margin: 0;"> <span id="LC2683" class="line" lang="plaintext">present exactly the same percentage of identity, the number of hits</span>
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<td class="diff-line-num old_line" data-linenumber="2385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2385
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2684
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<pre style="margin: 0;"> <span id="LC2684" class="line" lang="plaintext">reported is controlled by the \-\-maxaccepts value (1 by default).</span>
</pre>
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2685
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<pre style="margin: 0;">+<span id="LC2685" class="line" lang="plaintext">.TAG uc</span>
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2386
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2686
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<pre style="margin: 0;"> <span id="LC2686" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2387
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2687
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<pre style="margin: 0;"> <span id="LC2687" class="line" lang="plaintext">.BI \-\-uc \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="2388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2388
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2688
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<pre style="margin: 0;"> <span id="LC2688" class="line" lang="plaintext">Output searching results in \fIfilename\fR using a tab-separated</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2424" style="width: 35px; color: rgba(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="2724" style="width: 35px; color: rgba(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">@@ -2424,26 +2724,31 @@ Label of the query sequence.</td>
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<td class="diff-line-num old_line" data-linenumber="2424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2424
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<td class="diff-line-num new_line" data-linenumber="2724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2724
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<pre style="margin: 0;"> <span id="LC2724" class="line" lang="plaintext">Label of the target centroid sequence. Set to '*' for N.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2425
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2725
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<pre style="margin: 0;"> <span id="LC2725" class="line" lang="plaintext">.RE</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2426
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<td class="diff-line-num new_line" data-linenumber="2726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2726
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<pre style="margin: 0;"> <span id="LC2726" class="line" lang="plaintext">.RE</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2727
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<pre style="margin: 0;">+<span id="LC2727" class="line" lang="plaintext">.TAG uc_allhits</span>
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<td class="diff-line-num old_line" data-linenumber="2427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2427
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<td class="diff-line-num new_line" data-linenumber="2728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2728
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<pre style="margin: 0;"> <span id="LC2728" class="line" lang="plaintext">.TP</span>
</pre>
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2428
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<td class="diff-line-num new_line" data-linenumber="2729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2729
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<pre style="margin: 0;"> <span id="LC2729" class="line" lang="plaintext">.B \-\-uc_allhits</span>
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2429
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<td class="diff-line-num new_line" data-linenumber="2730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2730
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<pre style="margin: 0;"> <span id="LC2730" class="line" lang="plaintext">When using the \-\-uc option, show all hits, not just the top hit for</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2430
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<td class="diff-line-num new_line" data-linenumber="2731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2731
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<pre style="margin: 0;"> <span id="LC2731" class="line" lang="plaintext">each query.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2431" style="width: 35px; color: rgba(0,0,0,0.3); 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="2732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2732
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<pre style="margin: 0;">+<span id="LC2732" class="line" lang="plaintext">.TAG usearch_global</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2431
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<td class="diff-line-num new_line" data-linenumber="2733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2733
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<pre style="margin: 0;"> <span id="LC2733" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2432
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<td class="diff-line-num new_line" data-linenumber="2734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2734
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<pre style="margin: 0;"> <span id="LC2734" class="line" lang="plaintext">.BI \-\-usearch_global \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2433
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<td class="diff-line-num new_line" data-linenumber="2735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2735
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2735" class="line" lang="plaintext">Compare target sequences (\-\-db) to the fasta-formatted query</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2434
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<td class="diff-line-num new_line" data-linenumber="2736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2736
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2736" class="line" lang="plaintext">sequences contained in \fIfilename\fR, using global pairwise</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2435
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<td class="diff-line-num new_line" data-linenumber="2737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2737
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2737" class="line" lang="plaintext">alignment.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2738
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<pre style="margin: 0;">+<span id="LC2738" class="line" lang="plaintext">.TAG userfields</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2436
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<td class="diff-line-num new_line" data-linenumber="2739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2739
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2739" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2437
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<td class="diff-line-num new_line" data-linenumber="2740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2740
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<pre style="margin: 0;"> <span id="LC2740" class="line" lang="plaintext">.BI \-\-userfields \0string</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2438
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<td class="diff-line-num new_line" data-linenumber="2741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2741
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2741" class="line" lang="plaintext">When using \-\-userout, select and order the fields written to the</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="2439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2439
</td>
<td class="diff-line-num new_line" data-linenumber="2742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2742
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2742" class="line" lang="plaintext">output file. Fields are separated by '+' (e.g. query+target+id). See</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="2440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2440
</td>
<td class="diff-line-num new_line" data-linenumber="2743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2743
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2743" class="line" lang="plaintext">the 'Userfields' section for a complete list of fields.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2744
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<pre style="margin: 0;">+<span id="LC2744" class="line" lang="plaintext">.TAG userout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2441
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<td class="diff-line-num new_line" data-linenumber="2745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2745
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2745" class="line" lang="plaintext">.TP</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="2442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2442
</td>
<td class="diff-line-num new_line" data-linenumber="2746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2746
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2746" class="line" lang="plaintext">.BI \-\-userout \0filename</span>
</pre>
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<td class="diff-line-num old_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
</td>
<td class="diff-line-num new_line" data-linenumber="2747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2747
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2747" class="line" lang="plaintext">Write user-defined tab-separated output to \fIfilename\fR. Select the</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="2444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2444
</td>
<td class="diff-line-num new_line" data-linenumber="2748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2748
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2748" class="line" lang="plaintext">fields with the option \-\-userfields. Output order may vary when</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="2445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2445
</td>
<td class="diff-line-num new_line" data-linenumber="2749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2749
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2749" class="line" lang="plaintext">using multiple threads. If \-\-userfields is empty or not present,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2446
</td>
<td class="diff-line-num new_line" data-linenumber="2750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2750
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2750" class="line" lang="plaintext">\fIfilename\fR is empty.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2751
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<pre style="margin: 0;">+<span id="LC2751" class="line" lang="plaintext">.TAG weak_id</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2447
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<td class="diff-line-num new_line" data-linenumber="2752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2752
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2752" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2448
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<td class="diff-line-num new_line" data-linenumber="2753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2753
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<pre style="margin: 0;"> <span id="LC2753" class="line" lang="plaintext">.BI \-\-weak_id \0real</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2449
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<td class="diff-line-num new_line" data-linenumber="2754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2754
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<pre style="margin: 0;"> <span id="LC2754" class="line" lang="plaintext">Show hits with percentage of identity of at least \fIreal\fR, without</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2453" style="width: 35px; color: rgba(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="2758" style="width: 35px; color: rgba(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">@@ -2453,6 +2758,7 @@ are found (as defined by \-\-maxaccepts, \-\-maxrejects, and</td>
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2453
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<td class="diff-line-num new_line" data-linenumber="2758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2758
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<pre style="margin: 0;"> <span id="LC2758" class="line" lang="plaintext">\-\-maxaccepts, high \-\-id values can be used, hence preserving both</span>
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2454
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2759
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<pre style="margin: 0;"> <span id="LC2759" class="line" lang="plaintext">speed and sensitivity. Logically, \fIreal\fR must be smaller than the</span>
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<td class="diff-line-num old_line" data-linenumber="2455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2455
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2760
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<pre style="margin: 0;"> <span id="LC2760" class="line" lang="plaintext">value indicated by \-\-id.</span>
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<td class="diff-line-num new old_line" data-linenumber="2456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2761
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<pre style="margin: 0;">+<span id="LC2761" class="line" lang="plaintext">.TAG wordlength</span>
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<td class="diff-line-num old_line" data-linenumber="2456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2456
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<td class="diff-line-num new_line" data-linenumber="2762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2762
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<pre style="margin: 0;"> <span id="LC2762" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="2457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2457
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<td class="diff-line-num new_line" data-linenumber="2763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2763
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<pre style="margin: 0;"> <span id="LC2763" class="line" lang="plaintext">.BI \-\-wordlength\~ "positive integer"</span>
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<td class="diff-line-num old_line" data-linenumber="2458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2458
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<td class="diff-line-num new_line" data-linenumber="2764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2764
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<pre style="margin: 0;"> <span id="LC2764" class="line" lang="plaintext">Length of words (i.e. \fIk\fR-mers) for database indexing. The range</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2469" style="width: 35px; color: rgba(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="2775" style="width: 35px; color: rgba(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">@@ -2469,26 +2775,32 @@ default value is 8.</td>
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2469
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2775
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<pre style="margin: 0;"> <span id="LC2775" class="line" lang="plaintext">.RE</span>
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<td class="diff-line-num old_line" data-linenumber="2470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2470
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<td class="diff-line-num new_line" data-linenumber="2776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2776
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<pre style="margin: 0;"> <span id="LC2776" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2471
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<td class="diff-line-num new_line" data-linenumber="2777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2777
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<pre style="margin: 0;"> <span id="LC2777" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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2778
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<pre style="margin: 0;">+<span id="LC2778" class="line" lang="plaintext">.TAG shuffling-options</span>
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<td class="diff-line-num old_line" data-linenumber="2472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2472
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<td class="diff-line-num new_line" data-linenumber="2779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2779
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<pre style="margin: 0;"> <span id="LC2779" class="line" lang="plaintext">Shuffling options:</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2473
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<td class="diff-line-num new_line" data-linenumber="2780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2780
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<pre style="margin: 0;"> <span id="LC2780" class="line" lang="plaintext">.RS</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2474
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<td class="diff-line-num new_line" data-linenumber="2781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2781
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<pre style="margin: 0;"> <span id="LC2781" class="line" lang="plaintext">Fasta entries in the input file are outputted in a pseudo-random</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2475
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<td class="diff-line-num new_line" data-linenumber="2782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2782
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<pre style="margin: 0;"> <span id="LC2782" class="line" lang="plaintext">order.</span>
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2783
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<pre style="margin: 0;">+<span id="LC2783" class="line" lang="plaintext">.TAG output</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2476
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2784
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<pre style="margin: 0;"> <span id="LC2784" class="line" lang="plaintext">.TP 9</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2477
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2785
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<pre style="margin: 0;"> <span id="LC2785" class="line" lang="plaintext">.BI \-\-output \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="2478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2478
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<td class="diff-line-num new_line" data-linenumber="2786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2786
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<pre style="margin: 0;"> <span id="LC2786" class="line" lang="plaintext">Write the shuffled sequences to \fIfilename\fR, in fasta format.</span>
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<td class="diff-line-num new old_line" data-linenumber="2479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2787
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<pre style="margin: 0;">+<span id="LC2787" class="line" lang="plaintext">.TAG randseed</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2479
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2788
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<pre style="margin: 0;"> <span id="LC2788" class="line" lang="plaintext">.TP</span>
</pre>
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2480
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<td class="diff-line-num new_line" data-linenumber="2789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2789
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<pre style="margin: 0;"> <span id="LC2789" class="line" lang="plaintext">.BI \-\-randseed\~ "positive integer"</span>
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2481
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<td class="diff-line-num new_line" data-linenumber="2790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2790
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<pre style="margin: 0;"> <span id="LC2790" class="line" lang="plaintext">When shuffling sequence order, use \fIinteger\fR as seed. A given seed</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2482
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<td class="diff-line-num new_line" data-linenumber="2791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2791
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<pre style="margin: 0;"> <span id="LC2791" class="line" lang="plaintext">always produces the same output order (useful for replicability). Set</span>
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<td class="diff-line-num old_line" data-linenumber="2483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2483
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<td class="diff-line-num new_line" data-linenumber="2792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2792
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<pre style="margin: 0;"> <span id="LC2792" class="line" lang="plaintext">to 0 to use a pseudo-random seed (default behavior).</span>
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<td class="diff-line-num new new_line" data-linenumber="2793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2793
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<pre style="margin: 0;">+<span id="LC2793" class="line" lang="plaintext">.TAG relabel</span>
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2484
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<td class="diff-line-num new_line" data-linenumber="2794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2794
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<pre style="margin: 0;"> <span id="LC2794" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2485
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<td class="diff-line-num new_line" data-linenumber="2795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2795
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<pre style="margin: 0;"> <span id="LC2795" class="line" lang="plaintext">.BI \-\-relabel \0string</span>
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<td class="diff-line-num old_line" data-linenumber="2486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2486
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<td class="diff-line-num new_line" data-linenumber="2796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2796
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<pre style="margin: 0;"> <span id="LC2796" class="line" lang="plaintext">Relabel sequences using the prefix \fIstring\fR and a ticker (1, 2, 3,</span>
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<td class="diff-line-num old_line" data-linenumber="2487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2487
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<td class="diff-line-num new_line" data-linenumber="2797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2797
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<pre style="margin: 0;"> <span id="LC2797" class="line" lang="plaintext">etc.) to construct the new headers. Use \-\-sizeout to conserve the</span>
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<td class="diff-line-num old_line" data-linenumber="2488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2488
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<td class="diff-line-num new_line" data-linenumber="2798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2798
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<pre style="margin: 0;"> <span id="LC2798" class="line" lang="plaintext">abundance annotations.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2489" style="width: 35px; color: rgba(0,0,0,0.3); 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="2799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2799
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<pre style="margin: 0;">+<span id="LC2799" class="line" lang="plaintext">.TAG relabel_keep</span>
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<td class="diff-line-num old_line" data-linenumber="2489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2489
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<td class="diff-line-num new_line" data-linenumber="2800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2800
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<pre style="margin: 0;"> <span id="LC2800" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2490
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<td class="diff-line-num new_line" data-linenumber="2801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2801
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<pre style="margin: 0;"> <span id="LC2801" class="line" lang="plaintext">.B \-\-relabel_keep</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2491
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<td class="diff-line-num new_line" data-linenumber="2802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2802
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<pre style="margin: 0;"> <span id="LC2802" class="line" lang="plaintext">When relabelling, keep the old identifier in the header after a space.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2492" style="width: 35px; color: rgba(0,0,0,0.3); 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="2803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2803
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<pre style="margin: 0;">+<span id="LC2803" class="line" lang="plaintext">.TAG relabel_md5</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2492
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<td class="diff-line-num new_line" data-linenumber="2804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2804
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<pre style="margin: 0;"> <span id="LC2804" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2493
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<td class="diff-line-num new_line" data-linenumber="2805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2805
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<pre style="margin: 0;"> <span id="LC2805" class="line" lang="plaintext">.B \-\-relabel_md5</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2494
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<td class="diff-line-num new_line" data-linenumber="2806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2806
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2806" class="line" lang="plaintext">Relabel sequences using the MD5 message digest algorithm applied to</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2502" style="width: 35px; color: rgba(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="2814" style="width: 35px; color: rgba(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">@@ -2502,6 +2814,11 @@ inputs give the same result. The MD5 digest generates a 128-bit</td>
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<td class="diff-line-num old_line" data-linenumber="2502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2502
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<td class="diff-line-num new_line" data-linenumber="2814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2814
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2814" class="line" lang="plaintext">(16-byte) digest that is represented by 16 hexadecimal numbers (using</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2503
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<td class="diff-line-num new_line" data-linenumber="2815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2815
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<pre style="margin: 0;"> <span id="LC2815" class="line" lang="plaintext">32 symbols among 0123456789abcdef). Use \-\-sizeout to conserve the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2504
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<td class="diff-line-num new_line" data-linenumber="2816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2816
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2816" class="line" lang="plaintext">abundance annotations.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2817
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<pre style="margin: 0;">+<span id="LC2817" class="line" lang="plaintext">.TAG relabel_self</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2505" style="width: 35px; color: rgba(0,0,0,0.3); 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="2818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2818
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<pre style="margin: 0;">+<span id="LC2818" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2819
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<pre style="margin: 0;">+<span id="LC2819" class="line" lang="plaintext">.B \-\-relabel_self</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2820
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<pre style="margin: 0;">+<span id="LC2820" class="line" lang="plaintext">Relabel sequences using the sequence itself as the label.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2821
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<pre style="margin: 0;">+<span id="LC2821" class="line" lang="plaintext">.TAG relabel_sha1</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2505
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<td class="diff-line-num new_line" data-linenumber="2822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2822
</td>
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<pre style="margin: 0;"> <span id="LC2822" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2506
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<td class="diff-line-num new_line" data-linenumber="2823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2823
</td>
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<pre style="margin: 0;"> <span id="LC2823" class="line" lang="plaintext">.B \-\-relabel_sha1</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2507
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<td class="diff-line-num new_line" data-linenumber="2824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2824
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2824" class="line" lang="plaintext">Relabel sequences using the SHA1 message digest algorithm applied to</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2512" style="width: 35px; color: rgba(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="2829" style="width: 35px; color: rgba(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">@@ -2512,19 +2829,23 @@ hexadecimal numbers (40 symbols). The probability of a collision (two</td>
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<td class="diff-line-num old_line" data-linenumber="2512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2512
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<td class="diff-line-num new_line" data-linenumber="2829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2829
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<pre style="margin: 0;"> <span id="LC2829" class="line" lang="plaintext">non-identical sequences having the same digest) is smaller for the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2513
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<td class="diff-line-num new_line" data-linenumber="2830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2830
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2830" class="line" lang="plaintext">SHA1 algorithm than it is for the MD5 algorithm. Use \-\-sizeout to</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2514
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<td class="diff-line-num new_line" data-linenumber="2831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2831
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<pre style="margin: 0;"> <span id="LC2831" class="line" lang="plaintext">conserve the abundance annotations.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2515" style="width: 35px; color: rgba(0,0,0,0.3); 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="2832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2832
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<pre style="margin: 0;">+<span id="LC2832" class="line" lang="plaintext">.TAG sizeout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2515
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<td class="diff-line-num new_line" data-linenumber="2833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2833
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<pre style="margin: 0;"> <span id="LC2833" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2516
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<td class="diff-line-num new_line" data-linenumber="2834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2834
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<pre style="margin: 0;"> <span id="LC2834" class="line" lang="plaintext">.B \-\-sizeout</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2517
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<td class="diff-line-num new_line old" data-linenumber="2835" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2517" class="line" lang="plaintext">When using \-\-relabel, \-\-relabel_md5 or \-\-relabel_sha1, preserve</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2518
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<td class="diff-line-num new_line old" data-linenumber="2835" style="width: 35px; color: rgba(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="LC2518" class="line" lang="plaintext">and report abundance annotations to the output fasta file (using the</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2519
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<td class="diff-line-num new_line old" data-linenumber="2835" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2519" class="line" lang="plaintext">pattern ';size=\fIinteger\fR;').</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2835
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<pre style="margin: 0;">+<span id="LC2835" class="line" lang="plaintext">When using \-\-relabel, \-\-relabel_self, \-\-relabel_md5 or</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2836
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<pre style="margin: 0;">+<span id="LC2836" class="line" lang="plaintext">\-\-relabel_sha1, preserve and report abundance annotations to the</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2837
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<pre style="margin: 0;">+<span id="LC2837" class="line" lang="plaintext">output fasta file (using the pattern ';size=\fIinteger\fR;').</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2838
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<pre style="margin: 0;">+<span id="LC2838" class="line" lang="plaintext">.TAG shuffle</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2520
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<td class="diff-line-num new_line" data-linenumber="2839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2839
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2839" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2521
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<td class="diff-line-num new_line" data-linenumber="2840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2840
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2840" class="line" lang="plaintext">.BI \-\-shuffle \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2522
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<td class="diff-line-num new_line" data-linenumber="2841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2841
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2841" class="line" lang="plaintext">Pseudo-randomly shuffle the order of sequences contained in</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2523
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<td class="diff-line-num new_line" data-linenumber="2842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2842
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2842" class="line" lang="plaintext">\fIfilename\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2843
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<pre style="margin: 0;">+<span id="LC2843" class="line" lang="plaintext">.TAG topn</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2524
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<td class="diff-line-num new_line" data-linenumber="2844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2844
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2844" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2525
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<td class="diff-line-num new_line" data-linenumber="2845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2845
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2845" class="line" lang="plaintext">.BI \-\-topn\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2526
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<td class="diff-line-num new_line" data-linenumber="2846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2846
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2846" class="line" lang="plaintext">Output only the first \fIinteger\fR sequences after pseudo-random</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2527
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<td class="diff-line-num new_line" data-linenumber="2847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2847
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2847" class="line" lang="plaintext">reordering.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2848
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<pre style="margin: 0;">+<span id="LC2848" class="line" lang="plaintext">.TAG xsize</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2528
</td>
<td class="diff-line-num new_line" data-linenumber="2849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2849
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2849" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2529
</td>
<td class="diff-line-num new_line" data-linenumber="2850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2850
</td>
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<pre style="margin: 0;"> <span id="LC2850" class="line" lang="plaintext">.B \-\-xsize</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2530
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<td class="diff-line-num new_line" data-linenumber="2851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2851
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2851" class="line" lang="plaintext">Strip abundance information from the headers when writing the output</span>
</pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2532,6 +2853,7 @@ file.</td>
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2532
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2853
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<pre style="margin: 0;"> <span id="LC2853" class="line" lang="plaintext">.RE</span>
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2533
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2854
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<pre style="margin: 0;"> <span id="LC2854" class="line" lang="plaintext">.PP</span>
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2534
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2855
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<pre style="margin: 0;"> <span id="LC2855" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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2856
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<pre style="margin: 0;">+<span id="LC2856" class="line" lang="plaintext">.TAG sorting-options</span>
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<td class="diff-line-num old_line" data-linenumber="2535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2535
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2857
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<pre style="margin: 0;"> <span id="LC2857" class="line" lang="plaintext">Sorting options:</span>
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<td class="diff-line-num old_line" data-linenumber="2536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2536
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<td class="diff-line-num new_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">
2858
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<pre style="margin: 0;"> <span id="LC2858" class="line" lang="plaintext">.RS</span>
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<td class="diff-line-num old_line" data-linenumber="2537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2537
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2859
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<pre style="margin: 0;"> <span id="LC2859" class="line" lang="plaintext">Fasta entries are sorted by decreasing abundance (\-\-sortbysize) or</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2544" style="width: 35px; color: rgba(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="2866" style="width: 35px; color: rgba(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">@@ -2544,51 +2866,68 @@ sorting performed during chimera checking (\-\-uchime_denovo),</td>
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2544
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2866
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<pre style="margin: 0;"> <span id="LC2866" class="line" lang="plaintext">dereplication (\-\-derep_fulllength), and clustering (\-\-cluster_fast</span>
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2545
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2867
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<pre style="margin: 0;"> <span id="LC2867" class="line" lang="plaintext">and \-\-cluster_size).</span>
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<td class="diff-line-num old_line" data-linenumber="2546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2546
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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="plaintext">.PP</span>
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<td class="diff-line-num new old_line" data-linenumber="2547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2869
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<pre style="margin: 0;">+<span id="LC2869" class="line" lang="plaintext">.TAG maxsize</span>
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<td class="diff-line-num old_line" data-linenumber="2547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2547
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2870
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<pre style="margin: 0;"> <span id="LC2870" class="line" lang="plaintext">.TP 9</span>
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<td class="diff-line-num old_line" data-linenumber="2548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2548
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2871
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<pre style="margin: 0;"> <span id="LC2871" class="line" lang="plaintext">.BI \-\-maxsize\~ "positive integer"</span>
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<td class="diff-line-num old_line" data-linenumber="2549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2549
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2872
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<pre style="margin: 0;"> <span id="LC2872" class="line" lang="plaintext">When using \-\-sortbysize, discard sequences with an abundance value</span>
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<td class="diff-line-num old_line" data-linenumber="2550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2550
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2873
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<pre style="margin: 0;"> <span id="LC2873" class="line" lang="plaintext">greater than \fIinteger\fR.</span>
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<td class="diff-line-num new old_line" data-linenumber="2551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2874
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<pre style="margin: 0;">+<span id="LC2874" class="line" lang="plaintext">.TAG minsize</span>
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<td class="diff-line-num old_line" data-linenumber="2551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2551
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2875
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<pre style="margin: 0;"> <span id="LC2875" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="2552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2552
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<td class="diff-line-num new_line" data-linenumber="2876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2876
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<pre style="margin: 0;"> <span id="LC2876" class="line" lang="plaintext">.BI \-\-minsize\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2553
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<td class="diff-line-num new_line" data-linenumber="2877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2877
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<pre style="margin: 0;"> <span id="LC2877" class="line" lang="plaintext">When using \-\-sortbysize, discard sequences with an abundance value</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2554
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<td class="diff-line-num new_line" data-linenumber="2878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2878
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<pre style="margin: 0;"> <span id="LC2878" class="line" lang="plaintext">smaller than \fIinteger\fR.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2555" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="plaintext">.TAG output</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2555
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<td class="diff-line-num new_line" data-linenumber="2880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2880
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2880" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2556
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<td class="diff-line-num new_line" data-linenumber="2881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2881
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<pre style="margin: 0;"> <span id="LC2881" class="line" lang="plaintext">.BI \-\-output \0filename</span>
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<td class="diff-line-num old_line" data-linenumber="2557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2557
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<td class="diff-line-num new_line" data-linenumber="2882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2882
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<pre style="margin: 0;"> <span id="LC2882" class="line" lang="plaintext">Write the sorted sequences to \fIfilename\fR, in fasta format.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2558" style="width: 35px; color: rgba(0,0,0,0.3); 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="2883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2883
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2883" class="line" lang="plaintext">.TAG relabel</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2558
</td>
<td class="diff-line-num new_line" data-linenumber="2884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2884
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2884" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2559
</td>
<td class="diff-line-num new_line" data-linenumber="2885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2885
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2885" class="line" lang="plaintext">.BI \-\-relabel \0string</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2560
</td>
<td class="diff-line-num new_line" data-linenumber="2886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2886
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2886" class="line" lang="plaintext">Please see the description of the same option under Chimera detection</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2561
</td>
<td class="diff-line-num new_line" data-linenumber="2887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2887
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2887" class="line" lang="plaintext">for details.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2888" class="line" lang="plaintext">.TAG relabel_keep</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2562
</td>
<td class="diff-line-num new_line" data-linenumber="2889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2889
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2889" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2563
</td>
<td class="diff-line-num new_line" data-linenumber="2890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2890
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2890" class="line" lang="plaintext">.B \-\-relabel_keep</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2564
</td>
<td class="diff-line-num new_line" data-linenumber="2891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2891
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2891" class="line" lang="plaintext">When relabelling, keep the old identifier in the header after a space.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2892" class="line" lang="plaintext">.TAG relabel_md5</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2565
</td>
<td class="diff-line-num new_line" data-linenumber="2893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2893
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2893" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2566
</td>
<td class="diff-line-num new_line" data-linenumber="2894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2894
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2894" class="line" lang="plaintext">.BI \-\-relabel_md5</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2567
</td>
<td class="diff-line-num new_line" data-linenumber="2895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2895
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2895" class="line" lang="plaintext">Please see the description of the same option under Chimera detection</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2568
</td>
<td class="diff-line-num new_line" data-linenumber="2896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2896
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2896" class="line" lang="plaintext">for details.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2897
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2897" class="line" lang="plaintext">.TAG relabel_self</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2898
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2898" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2899
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2899" class="line" lang="plaintext">.BI \-\-relabel_self</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2900
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2900" class="line" lang="plaintext">Please see the description of the same option under Chimera detection</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2901
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2901" class="line" lang="plaintext">for details.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2902
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2902" class="line" lang="plaintext">.TAG relabel_sha1</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2569
</td>
<td class="diff-line-num new_line" data-linenumber="2903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2903
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2903" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2570
</td>
<td class="diff-line-num new_line" data-linenumber="2904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2904
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2904" class="line" lang="plaintext">.BI \-\-relabel_sha1</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2571
</td>
<td class="diff-line-num new_line" data-linenumber="2905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2905
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2905" class="line" lang="plaintext">Please see the description of the same option under Chimera detection</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2572
</td>
<td class="diff-line-num new_line" data-linenumber="2906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2906
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2906" class="line" lang="plaintext">for details.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2907
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2907" class="line" lang="plaintext">.TAG sizeout</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2573
</td>
<td class="diff-line-num new_line" data-linenumber="2908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2908
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2908" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2574
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<td class="diff-line-num new_line" data-linenumber="2909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2909
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<pre style="margin: 0;"> <span id="LC2909" class="line" lang="plaintext">.B \-\-sizeout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2575
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<td class="diff-line-num new_line" data-linenumber="2910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2910
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<pre style="margin: 0;"> <span id="LC2910" class="line" lang="plaintext">When using \-\-relabel, report abundance annotations to the output</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2576
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<td class="diff-line-num new_line" data-linenumber="2911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2911
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<pre style="margin: 0;"> <span id="LC2911" class="line" lang="plaintext">fasta file (using the pattern ';size=\fIinteger\fR;').</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2577" style="width: 35px; color: rgba(0,0,0,0.3); 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="2912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2912
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<pre style="margin: 0;">+<span id="LC2912" class="line" lang="plaintext">.TAG sortbylength</span>
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<td class="diff-line-num old_line" data-linenumber="2577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2577
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<td class="diff-line-num new_line" data-linenumber="2913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2913
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<pre style="margin: 0;"> <span id="LC2913" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2578
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<td class="diff-line-num new_line" data-linenumber="2914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2914
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<pre style="margin: 0;"> <span id="LC2914" class="line" lang="plaintext">.BI \-\-sortbylength \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2579
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<td class="diff-line-num new_line" data-linenumber="2915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2915
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<pre style="margin: 0;"> <span id="LC2915" class="line" lang="plaintext">Sort by decreasing length the sequences contained in</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2580
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<td class="diff-line-num new_line" data-linenumber="2916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2916
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<pre style="margin: 0;"> <span id="LC2916" class="line" lang="plaintext">\fIfilename\fR. See the general options \-\-minseqlength and</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2581
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<td class="diff-line-num new_line" data-linenumber="2917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2917
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<pre style="margin: 0;"> <span id="LC2917" class="line" lang="plaintext">\-\-maxseqlength to eliminate short and long sequences.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2918
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<pre style="margin: 0;">+<span id="LC2918" class="line" lang="plaintext">.TAG sortbysize</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2582
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<td class="diff-line-num new_line" data-linenumber="2919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2919
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2919" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2583
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<td class="diff-line-num new_line" data-linenumber="2920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2920
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<pre style="margin: 0;"> <span id="LC2920" class="line" lang="plaintext">.BI \-\-sortbysize \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2584
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<td class="diff-line-num new_line" data-linenumber="2921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2921
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<pre style="margin: 0;"> <span id="LC2921" class="line" lang="plaintext">Sort by decreasing abundance the sequences contained in \fIfilename\fR</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2585
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<td class="diff-line-num new_line" data-linenumber="2922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2922
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<pre style="margin: 0;"> <span id="LC2922" class="line" lang="plaintext">(missing abundance values are assumed to be ';size=1'). See the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2586
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<td class="diff-line-num new_line" data-linenumber="2923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2923
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2923" class="line" lang="plaintext">options \-\-minsize and \-\-maxsize to eliminate rare and dominant</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2587
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<td class="diff-line-num new_line" data-linenumber="2924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2924
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2924" class="line" lang="plaintext">sequences.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2588" style="width: 35px; color: rgba(0,0,0,0.3); 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="2925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2925
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<pre style="margin: 0;">+<span id="LC2925" class="line" lang="plaintext">.TAG topn</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2588
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<td class="diff-line-num new_line" data-linenumber="2926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2926
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2926" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2589
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<td class="diff-line-num new_line" data-linenumber="2927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2927
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<pre style="margin: 0;"> <span id="LC2927" class="line" lang="plaintext">.BI \-\-topn\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2590
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<td class="diff-line-num new_line" data-linenumber="2928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2928
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2928" class="line" lang="plaintext">Output only the top \fIinteger\fR sequences (i.e. the longest or the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2591
</td>
<td class="diff-line-num new_line" data-linenumber="2929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2929
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2929" class="line" lang="plaintext">most abundant).</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2930
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<pre style="margin: 0;">+<span id="LC2930" class="line" lang="plaintext">.TAG xsize</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2592
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<td class="diff-line-num new_line" data-linenumber="2931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2931
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2931" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2593
</td>
<td class="diff-line-num new_line" data-linenumber="2932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2932
</td>
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<pre style="margin: 0;"> <span id="LC2932" class="line" lang="plaintext">.B \-\-xsize</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2594
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<td class="diff-line-num new_line" data-linenumber="2933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2933
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<pre style="margin: 0;"> <span id="LC2933" class="line" lang="plaintext">Strip abundance information from the headers when writing the output</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2596" style="width: 35px; color: rgba(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="2935" style="width: 35px; color: rgba(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">@@ -2596,6 +2935,7 @@ file.</td>
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<td class="diff-line-num old_line" data-linenumber="2596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2596
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<td class="diff-line-num new_line" data-linenumber="2935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2935
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<pre style="margin: 0;"> <span id="LC2935" class="line" lang="plaintext">.RE</span>
</pre>
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2597
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<td class="diff-line-num new_line" data-linenumber="2936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2936
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<pre style="margin: 0;"> <span id="LC2936" class="line" lang="plaintext">.PP</span>
</pre>
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2598
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<td class="diff-line-num new_line" data-linenumber="2937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2937
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<pre style="margin: 0;"> <span id="LC2937" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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<td class="diff-line-num new old_line" data-linenumber="2599" style="width: 35px; color: rgba(0,0,0,0.3); 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="2938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2938
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<pre style="margin: 0;">+<span id="LC2938" class="line" lang="plaintext">.TAG subsampling-options</span>
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<td class="diff-line-num old_line" data-linenumber="2599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2599
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<td class="diff-line-num new_line" data-linenumber="2939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2939
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<pre style="margin: 0;"> <span id="LC2939" class="line" lang="plaintext">Subsampling options:</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2600
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<td class="diff-line-num new_line" data-linenumber="2940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2940
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<pre style="margin: 0;"> <span id="LC2940" class="line" lang="plaintext">.RS</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2601
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<td class="diff-line-num new_line" data-linenumber="2941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2941
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2941" class="line" lang="plaintext">Subsampling randomly extracts a certain number or a certain percentage</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2614" style="width: 35px; color: rgba(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="2954" style="width: 35px; color: rgba(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">@@ -2614,12 +2954,15 @@ with the options \-\-fasta_discarded and \-\-fastq_discarded. The</td>
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<td class="diff-line-num old_line" data-linenumber="2614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2614
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<td class="diff-line-num new_line" data-linenumber="2954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2954
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<pre style="margin: 0;"> <span id="LC2954" class="line" lang="plaintext">\-\-fastq_ascii, \-\-fastq_qmin and \-\-fastq_qmax options are also</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2615
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<td class="diff-line-num new_line" data-linenumber="2955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2955
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<pre style="margin: 0;"> <span id="LC2955" class="line" lang="plaintext">available.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2616
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<td class="diff-line-num new_line" data-linenumber="2956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2956
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2956" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2617" style="width: 35px; color: rgba(0,0,0,0.3); 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="2957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2957
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<pre style="margin: 0;">+<span id="LC2957" class="line" lang="plaintext">.TAG fastaout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2617
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<td class="diff-line-num new_line" data-linenumber="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2958
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2958" class="line" lang="plaintext">.TP 9</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2618
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<td class="diff-line-num new_line" data-linenumber="2959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2959
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2959" class="line" lang="plaintext">.BI \-\-fastaout \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2619
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<td class="diff-line-num new_line" data-linenumber="2960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2960
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2960" class="line" lang="plaintext">Write the sampled sequences to \fIfilename\fR, in fasta format.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2961
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<pre style="margin: 0;">+<span id="LC2961" class="line" lang="plaintext">.TAG fastaout_discarded</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2620
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<td class="diff-line-num new_line" data-linenumber="2962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2962
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2962" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2621
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<td class="diff-line-num new_line" data-linenumber="2963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2963
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2963" class="line" lang="plaintext">.BI \-\-fastaout_discarded \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2622
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<td class="diff-line-num new_line" data-linenumber="2964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2964
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2964" class="line" lang="plaintext">Write the sequences not sampled to \fIfilename\fR, in fasta format.</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="2623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2965
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<pre style="margin: 0;">+<span id="LC2965" class="line" lang="plaintext">.TAG fastq_ascii</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2623
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<td class="diff-line-num new_line" data-linenumber="2966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2966
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2966" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2624
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<td class="diff-line-num new_line" data-linenumber="2967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2967
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<pre style="margin: 0;"> <span id="LC2967" class="line" lang="plaintext">.BI \-\-fastq_ascii\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2625
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<td class="diff-line-num new_line" data-linenumber="2968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2968
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2968" class="line" lang="plaintext">Define the ASCII character number used as the basis for the FASTQ</span>
</pre>
</td>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2627" style="width: 35px; color: rgba(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="2970" style="width: 35px; color: rgba(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">@@ -2627,42 +2970,51 @@ quality score. The default is 33, which is used by the Sanger /</td>
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<td class="diff-line-num old_line" data-linenumber="2627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2627
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<td class="diff-line-num new_line" data-linenumber="2970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2970
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2970" class="line" lang="plaintext">Illumina 1.8+ FASTQ format (phred+33). The value 64 is used by the</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2628
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<td class="diff-line-num new_line" data-linenumber="2971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2971
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2971" class="line" lang="plaintext">Solexa, Illumina 1.3+ and Illumina 1.5+ formats (phred+64). Only 33</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2629
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<td class="diff-line-num new_line" data-linenumber="2972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2972
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2972" class="line" lang="plaintext">and 64 are valid arguments.</span>
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<td class="diff-line-num new new_line" data-linenumber="2973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2973
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<pre style="margin: 0;">+<span id="LC2973" class="line" lang="plaintext">.TAG fastq_qmax</span>
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<td class="diff-line-num old_line" data-linenumber="2630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2630
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<td class="diff-line-num new_line" data-linenumber="2974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2974
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<pre style="margin: 0;"> <span id="LC2974" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2631
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<td class="diff-line-num new_line" data-linenumber="2975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2975
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<pre style="margin: 0;"> <span id="LC2975" class="line" lang="plaintext">.BI \-\-fastq_qmax\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2632
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<td class="diff-line-num new_line" data-linenumber="2976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2976
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<pre style="margin: 0;"> <span id="LC2976" class="line" lang="plaintext">Specify the maximum quality score accepted when reading FASTQ</span>
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<td class="diff-line-num old_line" data-linenumber="2633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2633
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<td class="diff-line-num new_line" data-linenumber="2977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2977
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<pre style="margin: 0;"> <span id="LC2977" class="line" lang="plaintext">files. The default is 41, which is usual for recent Sanger/Illumina</span>
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<td class="diff-line-num old_line" data-linenumber="2634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2634
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<td class="diff-line-num new_line" data-linenumber="2978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2978
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<pre style="margin: 0;"> <span id="LC2978" class="line" lang="plaintext">1.8+ files.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2635" style="width: 35px; color: rgba(0,0,0,0.3); 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="2979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2979
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<pre style="margin: 0;">+<span id="LC2979" class="line" lang="plaintext">.TAG fastq_qmin</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2635
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<td class="diff-line-num new_line" data-linenumber="2980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2980
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<pre style="margin: 0;"> <span id="LC2980" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2636
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<td class="diff-line-num new_line" data-linenumber="2981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2981
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<pre style="margin: 0;"> <span id="LC2981" class="line" lang="plaintext">.BI \-\-fastq_qmin\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2637
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<td class="diff-line-num new_line" data-linenumber="2982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2982
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<pre style="margin: 0;"> <span id="LC2982" class="line" lang="plaintext">Specify the minimum quality score accepted for FASTQ files. The</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2638
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<td class="diff-line-num new_line" data-linenumber="2983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2983
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<pre style="margin: 0;"> <span id="LC2983" class="line" lang="plaintext">default is 0, which is usual for recent Sanger/Illumina 1.8+</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2639
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<td class="diff-line-num new_line" data-linenumber="2984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2984
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<pre style="margin: 0;"> <span id="LC2984" class="line" lang="plaintext">files. Older formats may use scores between -5 and 2.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2640" style="width: 35px; color: rgba(0,0,0,0.3); 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="2985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2985
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<pre style="margin: 0;">+<span id="LC2985" class="line" lang="plaintext">.TAG fastqout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2640
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<td class="diff-line-num new_line" data-linenumber="2986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2986
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<pre style="margin: 0;"> <span id="LC2986" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2641
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<td class="diff-line-num new_line" data-linenumber="2987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2987
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<pre style="margin: 0;"> <span id="LC2987" class="line" lang="plaintext">.BI \-\-fastqout \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2642
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<td class="diff-line-num new_line" data-linenumber="2988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2988
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2988" class="line" lang="plaintext">Write the sampled sequences to \fIfilename\fR, in fastq</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2643
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<td class="diff-line-num new_line" data-linenumber="2989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2989
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2989" class="line" lang="plaintext">format. Requires input in fastq format.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2644" style="width: 35px; color: rgba(0,0,0,0.3); 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="2990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2990
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<pre style="margin: 0;">+<span id="LC2990" class="line" lang="plaintext">.TAG fastqout_discarded</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2644
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<td class="diff-line-num new_line" data-linenumber="2991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2991
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2991" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2645
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<td class="diff-line-num new_line" data-linenumber="2992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2992
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<pre style="margin: 0;"> <span id="LC2992" class="line" lang="plaintext">.BI \-\-fastqout_discarded \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2646
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<td class="diff-line-num new_line" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2993
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2993" class="line" lang="plaintext">Write the sequences not sampled to \fIfilename\fR, in fastq</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="2647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2647
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<td class="diff-line-num new_line" data-linenumber="2994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2994
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2994" class="line" lang="plaintext">format. Requires input in fastq format.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2995
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<pre style="margin: 0;">+<span id="LC2995" class="line" lang="plaintext">.TAG fastx_subsample</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2648
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<td class="diff-line-num new_line" data-linenumber="2996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2996
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2996" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2649
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<td class="diff-line-num new_line" data-linenumber="2997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2997
</td>
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<pre style="margin: 0;"> <span id="LC2997" class="line" lang="plaintext">.BI \-\-fastx_subsample \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2650
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<td class="diff-line-num new_line" data-linenumber="2998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2998
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2998" class="line" lang="plaintext">Perform subsampling from the sequences in the specified input file</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2651
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<td class="diff-line-num new_line" data-linenumber="2999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2999
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<pre style="margin: 0;"> <span id="LC2999" class="line" lang="plaintext">that is in FASTA or FASTQ format.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2652" style="width: 35px; color: rgba(0,0,0,0.3); 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="3000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3000
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<pre style="margin: 0;">+<span id="LC3000" class="line" lang="plaintext">.TAG randseed</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2652
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<td class="diff-line-num new_line" data-linenumber="3001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3001
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<pre style="margin: 0;"> <span id="LC3001" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2653
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<td class="diff-line-num new_line" data-linenumber="3002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3002
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<pre style="margin: 0;"> <span id="LC3002" class="line" lang="plaintext">.BI \-\-randseed\~ "positive integer"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2654
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<td class="diff-line-num new_line" data-linenumber="3003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3003
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3003" class="line" lang="plaintext">Use \fIinteger\fR as a seed for the pseudo-random generator. A given</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2655
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<td class="diff-line-num new_line" data-linenumber="3004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3004
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<pre style="margin: 0;"> <span id="LC3004" class="line" lang="plaintext">seed always produces the same output, which is useful for</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2656
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<td class="diff-line-num new_line" data-linenumber="3005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3005
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3005" class="line" lang="plaintext">replicability. Set to 0 to use a pseudo-random seed (default</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2657
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<td class="diff-line-num new_line" data-linenumber="3006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3006
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3006" class="line" lang="plaintext">behavior).</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3007
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<pre style="margin: 0;">+<span id="LC3007" class="line" lang="plaintext">.TAG relabel</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2658
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<td class="diff-line-num new_line" data-linenumber="3008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3008
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<pre style="margin: 0;"> <span id="LC3008" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2659
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<td class="diff-line-num new_line" data-linenumber="3009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3009
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3009" class="line" lang="plaintext">.BI \-\-relabel \0string</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2660
</td>
<td class="diff-line-num new_line" data-linenumber="3010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3010
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3010" class="line" lang="plaintext">Relabel sequences using the prefix \fIstring\fR and a ticker (1, 2, 3,</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2661
</td>
<td class="diff-line-num new_line" data-linenumber="3011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3011
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3011" class="line" lang="plaintext">etc.) to construct the new headers. Use \-\-sizeout to conserve the</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="2662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2662
</td>
<td class="diff-line-num new_line" data-linenumber="3012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3012
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3012" class="line" lang="plaintext">abundance annotations.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3013
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<pre style="margin: 0;">+<span id="LC3013" class="line" lang="plaintext">.TAG relabel_keep</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2663
</td>
<td class="diff-line-num new_line" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3014
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3014" class="line" lang="plaintext">.TP</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="2664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2664
</td>
<td class="diff-line-num new_line" data-linenumber="3015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3015
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3015" class="line" lang="plaintext">.B \-\-relabel_keep</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2665
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<td class="diff-line-num new_line" data-linenumber="3016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3016
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3016" class="line" lang="plaintext">When relabelling, keep the old identifier in the header after a space.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3017
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<pre style="margin: 0;">+<span id="LC3017" class="line" lang="plaintext">.TAG relabel_md5</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2666
</td>
<td class="diff-line-num new_line" data-linenumber="3018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3018
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3018" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2667
</td>
<td class="diff-line-num new_line" data-linenumber="3019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3019
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3019" class="line" lang="plaintext">.B \-\-relabel_md5</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2668
</td>
<td class="diff-line-num new_line" data-linenumber="3020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3020
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3020" class="line" lang="plaintext">Relabel sequences using the MD5 message digest algorithm applied to</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2676" style="width: 35px; color: rgba(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="3028" style="width: 35px; color: rgba(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">@@ -2676,6 +3028,11 @@ inputs give the same result. The MD5 digest generates a 128-bit</td>
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<td class="diff-line-num old_line" data-linenumber="2676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2676
</td>
<td class="diff-line-num new_line" data-linenumber="3028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3028
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3028" class="line" lang="plaintext">(16-byte) digest that is represented by 16 hexadecimal numbers (using</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2677
</td>
<td class="diff-line-num new_line" data-linenumber="3029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3029
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3029" class="line" lang="plaintext">32 symbols among 0123456789abcdef). Use \-\-sizeout to conserve the</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="2678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2678
</td>
<td class="diff-line-num new_line" data-linenumber="3030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3030
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3030" class="line" lang="plaintext">abundance annotations.</span>
</pre>
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3031
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<pre style="margin: 0;">+<span id="LC3031" class="line" lang="plaintext">.TAG relabel_self</span>
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3032
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<pre style="margin: 0;">+<span id="LC3032" class="line" lang="plaintext">.TP</span>
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3033
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<pre style="margin: 0;">+<span id="LC3033" class="line" lang="plaintext">.B \-\-relabel_self</span>
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<td class="diff-line-num new new_line" data-linenumber="3034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3034
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<pre style="margin: 0;">+<span id="LC3034" class="line" lang="plaintext">Relabel sequences using the sequence itself as the label.</span>
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<td class="diff-line-num new new_line" data-linenumber="3035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3035
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<pre style="margin: 0;">+<span id="LC3035" class="line" lang="plaintext">.TAG relabel_sha1</span>
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2679
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3036
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<pre style="margin: 0;"> <span id="LC3036" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="2680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2680
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<td class="diff-line-num new_line" data-linenumber="3037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3037
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<pre style="margin: 0;"> <span id="LC3037" class="line" lang="plaintext">.B \-\-relabel_sha1</span>
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<td class="diff-line-num old_line" data-linenumber="2681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2681
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<td class="diff-line-num new_line" data-linenumber="3038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3038
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<pre style="margin: 0;"> <span id="LC3038" class="line" lang="plaintext">Relabel sequences using the SHA1 message digest algorithm applied to</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2686" style="width: 35px; color: rgba(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="3043" style="width: 35px; color: rgba(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">@@ -2686,20 +3043,25 @@ hexadecimal numbers (40 symbols). The probability of a collision (two</td>
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2686
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3043
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<pre style="margin: 0;"> <span id="LC3043" class="line" lang="plaintext">non-identical sequences having the same digest) is smaller for the</span>
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<td class="diff-line-num old_line" data-linenumber="2687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2687
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<td class="diff-line-num new_line" data-linenumber="3044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3044
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<pre style="margin: 0;"> <span id="LC3044" class="line" lang="plaintext">SHA1 algorithm than it is for the MD5 algorithm. Use \-\-sizeout to</span>
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<td class="diff-line-num old_line" data-linenumber="2688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2688
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<td class="diff-line-num new_line" data-linenumber="3045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3045
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<pre style="margin: 0;"> <span id="LC3045" class="line" lang="plaintext">conserve the abundance annotations.</span>
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3046
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<pre style="margin: 0;">+<span id="LC3046" class="line" lang="plaintext">.TAG sample_pct</span>
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2689
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3047
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<pre style="margin: 0;"> <span id="LC3047" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2690
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC3048" class="line" lang="plaintext">.BI \-\-sample_pct\~ "real"</span>
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<td class="diff-line-num old_line" data-linenumber="2691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2691
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3049
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<pre style="margin: 0;"> <span id="LC3049" class="line" lang="plaintext">Subsample the given percentage of the input sequences. Accepted values</span>
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<td class="diff-line-num old_line" data-linenumber="2692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2692
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC3050" class="line" lang="plaintext">range from 0.0 to 100.0.</span>
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3051
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<pre style="margin: 0;">+<span id="LC3051" class="line" lang="plaintext">.TAG sample_size</span>
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<td class="diff-line-num old_line" data-linenumber="2693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2693
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3052
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<pre style="margin: 0;"> <span id="LC3052" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="2694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2694
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3053
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<pre style="margin: 0;"> <span id="LC3053" class="line" lang="plaintext">.BI \-\-sample_size\~ "positive integer"</span>
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<td class="diff-line-num old_line" data-linenumber="2695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2695
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<td class="diff-line-num new_line" data-linenumber="3054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3054
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<pre style="margin: 0;"> <span id="LC3054" class="line" lang="plaintext">Extract the given number of sequences.</span>
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<td class="diff-line-num new old_line" data-linenumber="2696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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3055
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<pre style="margin: 0;">+<span id="LC3055" class="line" lang="plaintext">.TAG sizein</span>
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<td class="diff-line-num old_line" data-linenumber="2696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2696
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<td class="diff-line-num new_line" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3056
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<pre style="margin: 0;"> <span id="LC3056" class="line" lang="plaintext">.TP</span>
</pre>
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2697
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3057
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<pre style="margin: 0;"> <span id="LC3057" class="line" lang="plaintext">.B \-\-sizein</span>
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2698
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3058
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<pre style="margin: 0;"> <span id="LC3058" class="line" lang="plaintext">Take the abundance information of the input file into account,</span>
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<td class="diff-line-num old_line" data-linenumber="2699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2699
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<td class="diff-line-num new_line" data-linenumber="3059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3059
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<pre style="margin: 0;"> <span id="LC3059" class="line" lang="plaintext">otherwise the abundance of each sequence is considered to be 1.</span>
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3060
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<pre style="margin: 0;">+<span id="LC3060" class="line" lang="plaintext">.TAG sizeout</span>
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2700
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<td class="diff-line-num new_line" data-linenumber="3061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3061
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<pre style="margin: 0;"> <span id="LC3061" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="2701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2701
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3062
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<pre style="margin: 0;"> <span id="LC3062" class="line" lang="plaintext">.B \-\-sizeout</span>
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2702
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3063
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<pre style="margin: 0;"> <span id="LC3063" class="line" lang="plaintext">Write abundance information to the output file.</span>
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3064
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<pre style="margin: 0;">+<span id="LC3064" class="line" lang="plaintext">.TAG xsize</span>
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<td class="diff-line-num old_line" data-linenumber="2703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2703
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3065
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<pre style="margin: 0;"> <span id="LC3065" class="line" lang="plaintext">.TP</span>
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2704
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3066
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<pre style="margin: 0;"> <span id="LC3066" class="line" lang="plaintext">.B \-\-xsize</span>
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2705
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3067
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<pre style="margin: 0;"> <span id="LC3067" class="line" lang="plaintext">Strip abundance information from the headers when writing the output</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2707" style="width: 35px; color: rgba(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">@@ -2707,12 +3069,14 @@ file.</td>
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2707
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3069
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<pre style="margin: 0;"> <span id="LC3069" class="line" lang="plaintext">.RE</span>
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<td class="diff-line-num old_line" data-linenumber="2708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2708
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3070
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<pre style="margin: 0;"> <span id="LC3070" class="line" lang="plaintext">.PP</span>
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2709
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3071
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<pre style="margin: 0;"> <span id="LC3071" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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3072
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<pre style="margin: 0;">+<span id="LC3072" class="line" lang="plaintext">.TAG taxonomic-classification-options</span>
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2710
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3073
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<pre style="margin: 0;"> <span id="LC3073" class="line" lang="plaintext">Taxonomic classification options:</span>
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<td class="diff-line-num old_line" data-linenumber="2711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2711
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<td class="diff-line-num new_line" data-linenumber="3074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3074
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<pre style="margin: 0;"> <span id="LC3074" class="line" lang="plaintext">.RS</span>
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2712
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3075
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<pre style="margin: 0;"> <span id="LC3075" class="line" lang="plaintext">The vsearch command \-\-sintax will classify the input sequences</span>
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<td class="diff-line-num old_line" data-linenumber="2713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2713
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3076
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<pre style="margin: 0;"> <span id="LC3076" class="line" lang="plaintext">according to the Sintax algorithm as described by Robert Edgar (2016)</span>
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<td class="diff-line-num old_line" data-linenumber="2714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2714
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3077
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<pre style="margin: 0;"> <span id="LC3077" class="line" lang="plaintext">in SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS</span>
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2715
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<pre style="margin: 0;">-<span id="LC2715" class="line" lang="plaintext">sequences, BioRxiv, 074161. Preprint. doi: https://doi.org/10.1101/074161.</span>
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3078
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<pre style="margin: 0;">+<span id="LC3078" class="line" lang="plaintext">sequences, BioRxiv, 074161. Preprint. doi: 10.1101/074161</span>
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3079
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<pre style="margin: 0;">+<span id="LC3079" class="line" lang="plaintext">.URL https://doi.org/10.1101/074161 (link)</span>
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2716
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3080
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<pre style="margin: 0;"> <span id="LC3080" class="line" lang="plaintext">.PP</span>
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2717
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3081
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<pre style="margin: 0;"> <span id="LC3081" class="line" lang="plaintext">The name of the fasta file containing the input sequences to be</span>
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2718
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3082
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<pre style="margin: 0;"> <span id="LC3082" class="line" lang="plaintext">classified is given as an argument to the \-\-sintax command. The reference</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2733" style="width: 35px; color: rgba(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="3097" style="width: 35px; color: rgba(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">@@ -2733,20 +3097,24 @@ of the rank by one of the letters d (for domain) k (kingdom), p</td>
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2733
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3097
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<pre style="margin: 0;"> <span id="LC3097" class="line" lang="plaintext">(species). The letter is followed by a colon (:) and the name of that</span>
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2734
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<td class="diff-line-num new_line" data-linenumber="3098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3098
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<pre style="margin: 0;"> <span id="LC3098" class="line" lang="plaintext">rank. Commas and semicolons are not allowed in the name of the rank.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2735
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<td class="diff-line-num new_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">
3099
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<pre style="margin: 0;"> <span id="LC3099" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2736
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<td class="diff-line-num new_line old" data-linenumber="3100" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2736" class="line" lang="plaintext">Example: ">X80725_S000004313;<span class="idiff left right">tax=d:Bacteria,p:Proteobacteria,c:Gammaproteobacteria,o:Enterobacteriales,f:Enterobacteriaceae,g:Escherichia/Shigella,</span>s:Escherichia_coli".</span>
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<td class="diff-line-num new old_line" data-linenumber="2737" style="width: 35px; color: rgba(0,0,0,0.3); 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="3100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3100
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<pre style="margin: 0;">+<span id="LC3100" class="line" lang="plaintext">Example: ">X80725_S000004313;<span class="idiff left right">\:tax=d:Bacteria,\:p:Proteobacteria,\:c:Gammaproteobacteria,\:o:Enterobacteriales,\:f:Enterobacteriaceae,\:g:Escherichia/Shigella,\:</span>s:Escherichia_coli".</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2737
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<td class="diff-line-num new_line" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3101
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<pre style="margin: 0;"> <span id="LC3101" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2738" style="width: 35px; color: rgba(0,0,0,0.3); 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="3102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3102
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<pre style="margin: 0;">+<span id="LC3102" class="line" lang="plaintext">.TAG db</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2738
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<td class="diff-line-num new_line" data-linenumber="3103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3103
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<pre style="margin: 0;"> <span id="LC3103" class="line" lang="plaintext">.TP 9</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2739
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<td class="diff-line-num new_line" data-linenumber="3104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3104
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<pre style="margin: 0;"> <span id="LC3104" class="line" lang="plaintext">.BI \-\-db \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2740
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<td class="diff-line-num new_line" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3105
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3105" class="line" lang="plaintext">Read the reference sequences from \fIfilename\fR, in FASTA, FASTQ or</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2741
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<td class="diff-line-num new_line" data-linenumber="3106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3106
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3106" class="line" lang="plaintext">UDB format. These sequences needs to be annotated with taxonomy.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3107
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<pre style="margin: 0;">+<span id="LC3107" class="line" lang="plaintext">.TAG sintax_cutoff</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2742
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<td class="diff-line-num new_line" data-linenumber="3108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3108
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3108" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2743
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<td class="diff-line-num new_line" data-linenumber="3109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3109
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<pre style="margin: 0;"> <span id="LC3109" class="line" lang="plaintext">.BI \-\-sintax_cutoff\~ "real"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2744
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<td class="diff-line-num new_line" data-linenumber="3110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3110
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<pre style="margin: 0;"> <span id="LC3110" class="line" lang="plaintext">Specify a minimum level of bootstrap support for the taxonomic ranks</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2745
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<td class="diff-line-num new_line" data-linenumber="3111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3111
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<pre style="margin: 0;"> <span id="LC3111" class="line" lang="plaintext">that will be included in column 4 of the output file. For instance</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2746
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<td class="diff-line-num new_line" data-linenumber="3112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3112
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<pre style="margin: 0;"> <span id="LC3112" class="line" lang="plaintext">0.9, corresponding to 90%.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3113
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<pre style="margin: 0;">+<span id="LC3113" class="line" lang="plaintext">.TAG sintax</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2747
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<td class="diff-line-num new_line" data-linenumber="3114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3114
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3114" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2748
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<td class="diff-line-num new_line" data-linenumber="3115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3115
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<pre style="margin: 0;"> <span id="LC3115" class="line" lang="plaintext">.BI \-\-sintax \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2749
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<td class="diff-line-num new_line" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3116
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3116" class="line" lang="plaintext">Read the input sequences from \fIfilename\fR, in FASTA or FASTQ format.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3117
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<pre style="margin: 0;">+<span id="LC3117" class="line" lang="plaintext">.TAG tabbedout</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2750
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<td class="diff-line-num new_line" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3118
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<pre style="margin: 0;"> <span id="LC3118" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2751
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<td class="diff-line-num new_line" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3119
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<pre style="margin: 0;"> <span id="LC3119" class="line" lang="plaintext">.BI \-\-tabbedout \0filename</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2752
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<td class="diff-line-num new_line" data-linenumber="3120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3120
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3120" class="line" lang="plaintext">Write the results to \fIfilename\fR, in a tab-separated text</span>
</pre>
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</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2760" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2760,6 +3128,7 @@ the threshold.</td>
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<td class="diff-line-num old_line" data-linenumber="2760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2760
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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">.RE</span>
</pre>
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2761
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<td class="diff-line-num new_line" data-linenumber="3129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3129
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<pre style="margin: 0;"> <span id="LC3129" class="line" lang="plaintext">.PP</span>
</pre>
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2762
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3130
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<pre style="margin: 0;"> <span id="LC3130" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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3131
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<pre style="margin: 0;">+<span id="LC3131" class="line" lang="plaintext">.TAG udb-options</span>
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<td class="diff-line-num old_line" data-linenumber="2763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2763
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<td class="diff-line-num new_line" data-linenumber="3132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3132
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<pre style="margin: 0;"> <span id="LC3132" class="line" lang="plaintext">UDB options:</span>
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<td class="diff-line-num old_line" data-linenumber="2764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2764
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<td class="diff-line-num new_line" data-linenumber="3133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3133
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<pre style="margin: 0;"> <span id="LC3133" class="line" lang="plaintext">.RS</span>
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<td class="diff-line-num old_line" data-linenumber="2765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2765
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<td class="diff-line-num new_line" data-linenumber="3134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3134
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<pre style="margin: 0;"> <span id="LC3134" class="line" lang="plaintext">Databases to be used with the \-\-usearch_global command may be</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2771" style="width: 35px; color: rgba(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="3140" style="width: 35px; color: rgba(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">@@ -2771,6 +3140,7 @@ below can be used to create and inspect UDB files. An UDB file may be</td>
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<td class="diff-line-num old_line" data-linenumber="2771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2771
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<td class="diff-line-num new_line" data-linenumber="3140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3140
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<pre style="margin: 0;"> <span id="LC3140" class="line" lang="plaintext">specified with the \-\-db option instead of a FASTA formatted file</span>
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<td class="diff-line-num old_line" data-linenumber="2772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2772
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<td class="diff-line-num new_line" data-linenumber="3141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3141
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<pre style="margin: 0;"> <span id="LC3141" class="line" lang="plaintext">with the \-\-usearch_global command.</span>
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<td class="diff-line-num old_line" data-linenumber="2773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2773
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3142
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<pre style="margin: 0;"> <span id="LC3142" class="line" lang="plaintext">.PP</span>
</pre>
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3143
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<pre style="margin: 0;">+<span id="LC3143" class="line" lang="plaintext">.TAG dbmask</span>
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2774
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3144
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<pre style="margin: 0;"> <span id="LC3144" class="line" lang="plaintext">.TP 9</span>
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2775
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3145
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<pre style="margin: 0;"> <span id="LC3145" class="line" lang="plaintext">.BI \-\-dbmask\~ "none|dust|soft"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2776
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3146
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<pre style="margin: 0;"> <span id="LC3146" class="line" lang="plaintext">Specify the sequence masking method used with the \-\-makeudb_usearch</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2779" style="width: 35px; color: rgba(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="3149" style="width: 35px; color: rgba(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">@@ -2779,32 +3149,39 @@ is specified. When dust is specified, the DUST algorithm will be used</td>
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2779
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3149
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<pre style="margin: 0;"> <span id="LC3149" class="line" lang="plaintext">for masking low complexity regions (short repeats and skewed</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2780
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<td class="diff-line-num new_line" data-linenumber="3150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3150
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<pre style="margin: 0;"> <span id="LC3150" class="line" lang="plaintext">composition). Lower case letters in the input file will be masked when</span>
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<td class="diff-line-num old_line" data-linenumber="2781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2781
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3151
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<pre style="margin: 0;"> <span id="LC3151" class="line" lang="plaintext">soft is specified (soft masking).</span>
</pre>
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3152
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<pre style="margin: 0;">+<span id="LC3152" class="line" lang="plaintext">.TAG hardmask</span>
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2782
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3153
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<pre style="margin: 0;"> <span id="LC3153" class="line" lang="plaintext">.TP</span>
</pre>
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2783
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3154
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<pre style="margin: 0;"> <span id="LC3154" class="line" lang="plaintext">.B \-\-hardmask</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2784
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3155
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<pre style="margin: 0;"> <span id="LC3155" class="line" lang="plaintext">Mask sequences by replacing letters with N for the \-\-makeudb_usearch</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2785
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<td class="diff-line-num new_line" data-linenumber="3156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3156
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<pre style="margin: 0;"> <span id="LC3156" class="line" lang="plaintext">command. The default is to use lower case letters (soft masking).</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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3157
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<pre style="margin: 0;">+<span id="LC3157" class="line" lang="plaintext">.TAG makeudb_usearch</span>
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<td class="diff-line-num old_line" data-linenumber="2786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2786
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3158
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<pre style="margin: 0;"> <span id="LC3158" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2787
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<td class="diff-line-num new_line" data-linenumber="3159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3159
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<pre style="margin: 0;"> <span id="LC3159" class="line" lang="plaintext">.BI \-\-makeudb_usearch \0filename</span>
</pre>
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2788
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<td class="diff-line-num new_line" data-linenumber="3160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3160
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3160" class="line" lang="plaintext">Create an UDB database file from the FASTA-formatted sequences in the</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2789
</td>
<td class="diff-line-num new_line" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3161
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3161" class="line" lang="plaintext">file with the given \fIfilename\fR. The UDB database is written to the</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2790
</td>
<td class="diff-line-num new_line" data-linenumber="3162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3162
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3162" class="line" lang="plaintext">file specified with the \-\-output option.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3163
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3163" class="line" lang="plaintext">.TAG output</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2791
</td>
<td class="diff-line-num new_line" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3164
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3164" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2792
</td>
<td class="diff-line-num new_line" data-linenumber="3165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3165
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3165" class="line" lang="plaintext">.BI \-\-output \0filename</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2793
</td>
<td class="diff-line-num new_line" data-linenumber="3166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3166
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3166" class="line" lang="plaintext">Specify the \fIfilename\fR of a FASTA or UDB output file for the</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2794
</td>
<td class="diff-line-num new_line" data-linenumber="3167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3167
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3167" class="line" lang="plaintext">\-\-makeudb_usearch or the \-\-udb2fasta command, respectively.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3168
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3168" class="line" lang="plaintext">.TAG udb2fasta</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2795
</td>
<td class="diff-line-num new_line" data-linenumber="3169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3169
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3169" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2796
</td>
<td class="diff-line-num new_line" data-linenumber="3170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3170
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3170" class="line" lang="plaintext">.BI \-\-udb2fasta \0filename</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2797
</td>
<td class="diff-line-num new_line" data-linenumber="3171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3171
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3171" class="line" lang="plaintext">Read the UDB database in the file with the given \fIfilename\fR and</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2798
</td>
<td class="diff-line-num new_line" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3172
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3172" class="line" lang="plaintext">output the sequences in FASTA format in the file specified by the</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2799
</td>
<td class="diff-line-num new_line" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3173
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3173" class="line" lang="plaintext">\-\-output option.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3174
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3174" class="line" lang="plaintext">.TAG udbinfo</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2800
</td>
<td class="diff-line-num new_line" data-linenumber="3175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3175
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3175" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2801
</td>
<td class="diff-line-num new_line" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3176
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3176" class="line" lang="plaintext">.BI \-\-udbinfo \0filename</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2802
</td>
<td class="diff-line-num new_line" data-linenumber="3177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3177
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3177" class="line" lang="plaintext">Show information about the UDB database in the file with the given</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2803
</td>
<td class="diff-line-num new_line" data-linenumber="3178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3178
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3178" class="line" lang="plaintext">\fIfilename\fR.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3179
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3179" class="line" lang="plaintext">.TAG udbstats</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2804
</td>
<td class="diff-line-num new_line" data-linenumber="3180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3180
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3180" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2805
</td>
<td class="diff-line-num new_line" data-linenumber="3181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3181
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3181" class="line" lang="plaintext">.BI \-\-udbstats \0filename</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2806
</td>
<td class="diff-line-num new_line" data-linenumber="3182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3182
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3182" class="line" lang="plaintext">Report statistics about the indexed words in the UDB database in the</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2807
</td>
<td class="diff-line-num new_line" data-linenumber="3183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3183
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3183" class="line" lang="plaintext">file with the given \fIfilename\fR.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3184
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3184" class="line" lang="plaintext">.TAG wordlength</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2808
</td>
<td class="diff-line-num new_line" data-linenumber="3185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3185
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3185" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2809
</td>
<td class="diff-line-num new_line" data-linenumber="3186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3186
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<pre style="margin: 0;"> <span id="LC3186" class="line" lang="plaintext">.BI \-\-wordlength\~ "positive integer"</span>
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2810
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<td class="diff-line-num new_line" data-linenumber="3187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3187
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<pre style="margin: 0;"> <span id="LC3187" class="line" lang="plaintext">Specify the length of the words to be used when creating the UDB</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2813" style="width: 35px; color: rgba(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="3190" style="width: 35px; color: rgba(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">@@ -2813,6 +3190,7 @@ range from 3 to 15. The default is 8.</td>
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2813
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<td class="diff-line-num new_line" data-linenumber="3190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3190
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<pre style="margin: 0;"> <span id="LC3190" class="line" lang="plaintext">.RE</span>
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2814
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<td class="diff-line-num new_line" data-linenumber="3191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3191
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<pre style="margin: 0;"> <span id="LC3191" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num old_line" data-linenumber="2815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2815
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<td class="diff-line-num new_line" data-linenumber="3192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3192
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<pre style="margin: 0;"> <span id="LC3192" class="line" lang="plaintext">.\" ----------------------------------------------------------------------------</span>
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3193
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<pre style="margin: 0;">+<span id="LC3193" class="line" lang="plaintext">.TAG userfields</span>
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2816
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3194
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<pre style="margin: 0;"> <span id="LC3194" class="line" lang="plaintext">Userfields (fields accepted by the \-\-userfields option):</span>
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2817
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3195
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<pre style="margin: 0;"> <span id="LC3195" class="line" lang="plaintext">.RS</span>
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2818
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3196
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<pre style="margin: 0;"> <span id="LC3196" class="line" lang="plaintext">.TP 9</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3082" style="width: 35px; color: rgba(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="3460" style="width: 35px; color: rgba(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">@@ -3082,8 +3460,8 @@ iddef (clustering, pairwise alignment, searching)</td>
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3082
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3460
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<pre style="margin: 0;"> <span id="LC3460" class="line" lang="plaintext">.IP -</span>
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3083
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3461
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<pre style="margin: 0;"> <span id="LC3461" class="line" lang="plaintext">maxuniquesize (dereplication)</span>
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3084
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3462
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<pre style="margin: 0;"> <span id="LC3462" class="line" lang="plaintext">.IP -</span>
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3085
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<pre style="margin: 0;">-<span id="LC3085" class="line" lang="plaintext">relabel_md5<span class="idiff left right"> and relabel_sha1 (chimera detection, dereplication, FASTQ</span></span>
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3086
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<pre style="margin: 0;">-<span id="LC3086" class="line" lang="plaintext">processing, shuffling, sorting)</span>
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3463
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<pre style="margin: 0;">+<span id="LC3463" class="line" lang="plaintext">relabel_md5<span class="idiff left right">, relabel_self and relabel_sha1 (chimera detection,</span></span>
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3464
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<pre style="margin: 0;">+<span id="LC3464" class="line" lang="plaintext"><span class="idiff left right">dereplication, FASTQ </span>processing, shuffling, sorting)</span>
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3087
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3465
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<pre style="margin: 0;"> <span id="LC3465" class="line" lang="plaintext">.IP -</span>
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3088
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3466
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<pre style="margin: 0;"> <span id="LC3466" class="line" lang="plaintext">shuffle (shuffling)</span>
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3089
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3467
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<pre style="margin: 0;"> <span id="LC3467" class="line" lang="plaintext">.IP -</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3198" style="width: 35px; color: rgba(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="3576" style="width: 35px; color: rgba(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">@@ -3198,14 +3576,18 @@ Frédéric Mahé.</td>
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3198
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3576
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<pre style="margin: 0;"> <span id="LC3576" class="line" lang="plaintext">Rognes T, Flouri T, Nichols B, Quince C, Mahé F. (2016)</span>
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3199
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3577
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<pre style="margin: 0;"> <span id="LC3577" class="line" lang="plaintext">VSEARCH: a versatile open source tool for metagenomics.</span>
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3200
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3578
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<pre style="margin: 0;"> <span id="LC3578" class="line" lang="plaintext">\fIPeerJ\fR 4:e2584 doi: 10.7717/peerj.2584</span>
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3201
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<pre style="margin: 0;">-<span id="LC3201" class="line" lang="plaintext"><span class="idiff left right"><https://doi.org/10.7717/peerj.2584></span></span>
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3579
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<pre style="margin: 0;">+<span id="LC3579" class="line" lang="plaintext"><span class="idiff left right">.URL https://doi.org/10.7717/peerj.2584 (link)</span></span>
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<td class="diff-line-num old_line" data-linenumber="3202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3202
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<td class="diff-line-num new_line" data-linenumber="3580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3580
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<pre style="margin: 0;"> <span id="LC3580" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3203
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<td class="diff-line-num new_line" data-linenumber="3581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3581
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<pre style="margin: 0;"> <span id="LC3581" class="line" lang="plaintext">.\" ============================================================================</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3204
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<td class="diff-line-num new_line" data-linenumber="3582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3582
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<pre style="margin: 0;"> <span id="LC3582" class="line" lang="plaintext">.SH REPORTING BUGS</span>
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<td class="diff-line-num old_line" data-linenumber="3205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3205
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<td class="diff-line-num new_line" data-linenumber="3583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3583
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<pre style="margin: 0;"> <span id="LC3583" class="line" lang="plaintext">Submit suggestions and bug-reports at</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3206" style="width: 35px; color: rgba(0,0,0,0.3); 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="3584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3584
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<pre style="margin: 0;">+<span id="LC3584" class="line" lang="plaintext">.URL https://github.com/torognes/vsearch/issues (link)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3206
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<td class="diff-line-num new_line" data-linenumber="3585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3585
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<pre style="margin: 0;"> <span id="LC3585" class="line" lang="plaintext"><https://github.com/torognes/vsearch/issues>, send a pull request on</span>
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<td class="diff-line-num new old_line" data-linenumber="3207" style="width: 35px; color: rgba(0,0,0,0.3); 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="3586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3586
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<pre style="margin: 0;">+<span id="LC3586" class="line" lang="plaintext">.URL https://github.com/torognes/vsearch (link)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3207
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<td class="diff-line-num new_line" data-linenumber="3587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3587
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<pre style="margin: 0;"> <span id="LC3587" class="line" lang="plaintext"><https://github.com/torognes/vsearch>, or compose a friendly or</span>
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<td class="diff-line-num old old_line" data-linenumber="3208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3208
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<td class="diff-line-num new_line old" data-linenumber="3588" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3208" class="line" lang="plaintext">curmudgeont e-mail to Torbjørn Rognes <torognes@ifi.uio.no>.</span>
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<td class="diff-line-num new old_line" data-linenumber="3209" style="width: 35px; color: rgba(0,0,0,0.3); 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="3588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3588
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<pre style="margin: 0;">+<span id="LC3588" class="line" lang="plaintext">curmudgeont e-mail to Torbjørn Rognes</span>
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<td class="diff-line-num new old_line" data-linenumber="3209" style="width: 35px; color: rgba(0,0,0,0.3); 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="3589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3589
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<pre style="margin: 0;">+<span id="LC3589" class="line" lang="plaintext">.MTO torognes@ifi.uio.no (link)</span>
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<td class="diff-line-num new old_line" data-linenumber="3209" style="width: 35px; color: rgba(0,0,0,0.3); 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="3590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3590
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<pre style="margin: 0;">+<span id="LC3590" class="line" lang="plaintext"><torognes@ifi.uio.no>.</span>
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<td class="diff-line-num old_line" data-linenumber="3209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3209
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<td class="diff-line-num new_line" data-linenumber="3591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3591
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<pre style="margin: 0;"> <span id="LC3591" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num old_line" data-linenumber="3210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3210
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<td class="diff-line-num new_line" data-linenumber="3592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3592
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<pre style="margin: 0;"> <span id="LC3592" class="line" lang="plaintext">.\" ============================================================================</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3211
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<td class="diff-line-num new_line" data-linenumber="3593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3593
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3593" class="line" lang="plaintext">.SH AVAILABILITY</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3240" style="width: 35px; color: rgba(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="3622" style="width: 35px; color: rgba(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">@@ -3240,7 +3622,9 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</td>
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<td class="diff-line-num old_line" data-linenumber="3240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3240
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<td class="diff-line-num new_line" data-linenumber="3622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3622
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3622" class="line" lang="plaintext">GNU General Public License for more details.</span>
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<td class="diff-line-num old_line" data-linenumber="3241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3241
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<td class="diff-line-num new_line" data-linenumber="3623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3623
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3623" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3242
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<td class="diff-line-num new_line" data-linenumber="3624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3624
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3624" class="line" lang="plaintext">You should have received a copy of the GNU General Public License</span>
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<td class="diff-line-num old old_line" data-linenumber="3243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3243
</td>
<td class="diff-line-num new_line old" data-linenumber="3625" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3243" class="line" lang="plaintext">along with this program. If not, see <http://www.gnu.org/licenses/>.</span>
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<td class="diff-line-num new old_line" data-linenumber="3244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3625
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<pre style="margin: 0;">+<span id="LC3625" class="line" lang="plaintext">along with this program. If not, see</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3626
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<pre style="margin: 0;">+<span id="LC3626" class="line" lang="plaintext">.URL http://www.gnu.org/licenses/ (link)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3244" style="width: 35px; color: rgba(0,0,0,0.3); 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="3627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3627
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<pre style="margin: 0;">+<span id="LC3627" class="line" lang="plaintext"><http://www.gnu.org/licenses/>.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3244
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<td class="diff-line-num new_line" data-linenumber="3628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3628
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<pre style="margin: 0;"> <span id="LC3628" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3245
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<td class="diff-line-num new_line" data-linenumber="3629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3629
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<pre style="margin: 0;"> <span id="LC3629" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3246
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<td class="diff-line-num new_line" data-linenumber="3630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3630
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<pre style="margin: 0;"> <span id="LC3630" class="line" lang="plaintext">\fBThe BSD 2-Clause License\fR</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3297" style="width: 35px; color: rgba(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="3681" style="width: 35px; color: rgba(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">@@ -3297,17 +3681,18 @@ copyright Julian R. Seward.</td>
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<td class="diff-line-num old_line" data-linenumber="3297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3297
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<td class="diff-line-num new_line" data-linenumber="3681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3681
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<pre style="margin: 0;"> <span id="LC3681" class="line" lang="plaintext">.SH SEE ALSO</span>
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<td class="diff-line-num old_line" data-linenumber="3298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3298
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<td class="diff-line-num new_line" data-linenumber="3682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3682
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<pre style="margin: 0;"> <span id="LC3682" class="line" lang="plaintext">\fBswipe\fR, an extremely fast pairwise local (Smith-Waterman)</span>
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<td class="diff-line-num old_line" data-linenumber="3299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3299
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<td class="diff-line-num new_line" data-linenumber="3683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3683
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<pre style="margin: 0;"> <span id="LC3683" class="line" lang="plaintext">database search tool by Torbjørn Rognes, available at</span>
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<td class="diff-line-num new old_line" data-linenumber="3300" style="width: 35px; color: rgba(0,0,0,0.3); 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="3684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3684
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<pre style="margin: 0;">+<span id="LC3684" class="line" lang="plaintext">.URL https://github.com/torognes/swipe "(link)"</span>
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<td class="diff-line-num old_line" data-linenumber="3300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3300
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<td class="diff-line-num new_line" data-linenumber="3685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3685
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<pre style="margin: 0;"> <span id="LC3685" class="line" lang="plaintext"><https://github.com/torognes/swipe>.</span>
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<td class="diff-line-num old_line" data-linenumber="3301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3301
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<td class="diff-line-num new_line" data-linenumber="3686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3686
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<pre style="margin: 0;"> <span id="LC3686" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3302
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<td class="diff-line-num new_line" data-linenumber="3687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3687
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3687" class="line" lang="plaintext">\fBswarm\fR, a fast and accurate amplicon clustering method by</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3303
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<td class="diff-line-num new_line" data-linenumber="3688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3688
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<pre style="margin: 0;"> <span id="LC3688" class="line" lang="plaintext">Frédéric Mahé and Torbjørn Rognes, available at</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3304" style="width: 35px; color: rgba(0,0,0,0.3); 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="3689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3689
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<pre style="margin: 0;">+<span id="LC3689" class="line" lang="plaintext">.URL https://github.com/torognes/swarm "(link)"</span>
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<td class="diff-line-num old_line" data-linenumber="3304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3304
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<td class="diff-line-num new_line" data-linenumber="3690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3690
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<pre style="margin: 0;"> <span id="LC3690" class="line" lang="plaintext"><https://github.com/torognes/swarm>.</span>
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<td class="diff-line-num old_line" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3305
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<td class="diff-line-num new_line" data-linenumber="3691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3691
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<pre style="margin: 0;"> <span id="LC3691" class="line" lang="plaintext">.PP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3306
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<td class="diff-line-num new_line" data-linenumber="3692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3692
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<pre style="margin: 0;"> <span id="LC3692" class="line" lang="plaintext">.\" ============================================================================</span>
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<td class="diff-line-num old_line" data-linenumber="3307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3307
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<td class="diff-line-num new_line" data-linenumber="3693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3693
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<pre style="margin: 0;"> <span id="LC3693" class="line" lang="plaintext">.SH VERSION HISTORY</span>
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<td class="diff-line-num old_line" data-linenumber="3308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3308
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<td class="diff-line-num new_line" data-linenumber="3694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3694
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<pre style="margin: 0;"> <span id="LC3694" class="line" lang="plaintext">New features and important modifications of \fBvsearch\fR (short lived</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3309
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<td class="diff-line-num new_line" data-linenumber="3695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3695
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<pre style="margin: 0;"> <span id="LC3695" class="line" lang="plaintext">or minor bug releases may not be mentioned):</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="3310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3310
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<td class="diff-line-num new_line old" data-linenumber="3696" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3310" class="line" lang="plaintext">.RS</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3311
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<td class="diff-line-num new_line" data-linenumber="3696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3696
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3696" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3312
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<td class="diff-line-num new_line" data-linenumber="3697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3697
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3697" class="line" lang="plaintext">.BR v1.0.0\~ "released November 28th, 2014"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3313
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<td class="diff-line-num new_line" data-linenumber="3698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3698
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3698" class="line" lang="plaintext">First public release.</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3844" style="width: 35px; color: rgba(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="4229" style="width: 35px; color: rgba(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">@@ -3844,7 +4229,17 @@ output from the fastq_stats command if quiet option was given. Updated manual.</td>
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<td class="diff-line-num old_line" data-linenumber="3844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3844
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<td class="diff-line-num new_line" data-linenumber="4229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4229
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<pre style="margin: 0;"> <span id="LC4229" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3845
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<td class="diff-line-num new_line" data-linenumber="4230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4230
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4230" class="line" lang="plaintext">.BR v2.13.6\~ "released July 2nd, 2019"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3846
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<td class="diff-line-num new_line" data-linenumber="4231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4231
</td>
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<pre style="margin: 0;"> <span id="LC4231" class="line" lang="plaintext">Added info about cut command to output of help command.</span>
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<td class="diff-line-num old old_line" data-linenumber="3847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3847
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<td class="diff-line-num new_line old" data-linenumber="4232" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3847" class="line" lang="plaintext">.RE</span>
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<td class="diff-line-num new old_line" data-linenumber="3848" style="width: 35px; color: rgba(0,0,0,0.3); 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="4232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4232
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<pre style="margin: 0;">+<span id="LC4232" class="line" lang="plaintext">.TP</span>
</pre>
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4233
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<pre style="margin: 0;">+<span id="LC4233" class="line" lang="plaintext">.BR v2.13.7\~ "released September 2nd, 2019"</span>
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4234
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<pre style="margin: 0;">+<span id="LC4234" class="line" lang="plaintext">Fixed bug in consensus sequence introduced in version 2.13.0.</span>
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4235
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<pre style="margin: 0;">+<span id="LC4235" class="line" lang="plaintext">.TP</span>
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4236
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<pre style="margin: 0;">+<span id="LC4236" class="line" lang="plaintext">.BR v2.14.0\~ "released September 11th, 2019"</span>
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4237
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<pre style="margin: 0;">+<span id="LC4237" class="line" lang="plaintext">Added relabel_self option. Made fasta_width, sizein, sizeout and</span>
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4238
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<pre style="margin: 0;">+<span id="LC4238" class="line" lang="plaintext">relabelling options valid for certain commands.</span>
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4239
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<pre style="margin: 0;">+<span id="LC4239" class="line" lang="plaintext">.TP</span>
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4240
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<pre style="margin: 0;">+<span id="LC4240" class="line" lang="plaintext">.BR v2.14.1\~ "released September 18th, 2019"</span>
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4241
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<pre style="margin: 0;">+<span id="LC4241" class="line" lang="plaintext">Fixed bug with sequences written to file specified with fastaout_rev</span>
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4242
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<pre style="margin: 0;">+<span id="LC4242" class="line" lang="plaintext">for commands fastx_filter and fastq_filter.</span>
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3848
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4243
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<pre style="margin: 0;"> <span id="LC4243" class="line" lang="plaintext">.LP</span>
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3849
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4244
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<pre style="margin: 0;"> <span id="LC4244" class="line" lang="plaintext">.\" ============================================================================</span>
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3850
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4245
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<pre style="margin: 0;"> <span id="LC4245" class="line" lang="plaintext">.\" TODO:</span>
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<li id="d79e6705e3db119ee1bb6ad9670fe99b162c13b0">
<a href="https://salsa.debian.org/med-team/vsearch/commit/a6e84605ff4ae3d2eb2fe51571bda5469e368a1e#d79e6705e3db119ee1bb6ad9670fe99b162c13b0"><strong>src/cluster.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="338" style="width: 35px; color: rgba(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="338" style="width: 35px; color: rgba(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">@@ -338,6 +338,11 @@ char * relabel_otu(int clusterno, char * sequence, int seqlen)</td>
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338
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338
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">label</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;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">opt_relabel</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">21</span><span class="p">);</span></span>
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339
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s%d"</span><span class="p">,</span> <span class="n" style="color: #333;">opt_relabel</span><span class="p">,</span> <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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340
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"> <span class="p">}</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" 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_relabel_self</span><span class="p">)</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="p">{</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">label</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;">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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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="s" style="color: #d14;">"%.*s"</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">);</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="p">}</span></span>
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341
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346
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<pre style="margin: 0;"> <span id="LC346" 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_relabel_sha1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"> <span class="p">{</span></span>
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"> <span class="n" style="color: #333;">label</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;">LEN_HEX_DIG_SHA1</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">@@ -363,7 +368,7 @@ void cluster_core_results_hit(struct hit * best,</td>
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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_otutabout</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_mothur_shared_out</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_biomout</span><span class="p">)</span></span>
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365
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp"> <span class="p">{</span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_relabel</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_sha1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_md5</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_relabel</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_s<span class="idiff left">elf</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_relabel_s</span>ha1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_md5</span><span class="p">)</span></span>
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cpp"> <span class="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="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">relabel_otu</span><span class="p">(</span><span class="n" style="color: #333;">clusterno</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="n" style="color: #333;">db_getsequence</span><span class="p">(</span><span class="n" style="color: #333;">best</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target</span><span class="p">),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="433" style="width: 35px; color: rgba(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">@@ -433,7 +438,7 @@ void cluster_core_results_nohit(int clusterno,</td>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_otutabout</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_mothur_shared_out</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_biomout</span><span class="p">)</span></span>
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435
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440
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="cpp"> <span class="p">{</span></span>
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436
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_relabel</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_sha1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_md5</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_relabel</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_s<span class="idiff left">elf</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_relabel_s</span>ha1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_md5</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="cpp"> <span class="p">{</span></span>
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443
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">relabel_otu</span><span class="p">(</span><span class="n" style="color: #333;">clusterno</span><span class="p">,</span> <span class="n" style="color: #333;">qsequence</span><span class="p">,</span> <span class="n" style="color: #333;">qseqlen</span><span class="p">);</span></span>
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439
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444
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="cpp"> <span class="n" style="color: #333;">otutable_add</span><span class="p">(</span><span class="n" style="color: #333;">query_head</span><span class="p">,</span> <span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="n" style="color: #333;">qsize</span><span class="p">);</span></span>
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<li id="67ef99e491c4bda5d0c47f152cae53d18d7fbcd3">
<a href="https://salsa.debian.org/med-team/vsearch/commit/a6e84605ff4ae3d2eb2fe51571bda5469e368a1e#67ef99e491c4bda5d0c47f152cae53d18d7fbcd3"><strong>src/fasta.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="322" style="width: 35px; color: rgba(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="322" style="width: 35px; color: rgba(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">@@ -322,13 +322,19 @@ void fasta_print(FILE * fp, const char * hdr,</td>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">fasta_print_sequence</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">opt_fasta_width</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">fprint_seq_label</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span> <span 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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* normalize first? */</span></span>
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<pre style="margin: 0;">+<span id="LC328" 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;">len</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">fasta_print_general</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span></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;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq</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;">int</span> <span class="n" style="color: #333;">len</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC335" 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="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">header_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC331" 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="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ordinal</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ee</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">clustersize</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">@@ -341,7 +347,9 @@ void fasta_print_general(FILE * fp,</td>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prefix</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;">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;">prefix</span><span class="p">);</span></span>
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343
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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"></span>
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344
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_relabel_sha1</span><span class="p">)</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_relabel_self</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="n" style="color: #333;">fprint_seq_label</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
352
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<pre style="margin: 0;">+<span id="LC352" 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_relabel_sha1</span><span class="p">)</span></span>
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345
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353
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"> <span class="n" style="color: #333;">fprint_seq_digest_sha1</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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346
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354
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<pre style="margin: 0;"> <span id="LC354" 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_relabel_md5</span><span class="p">)</span></span>
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347
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<td class="diff-line-num new_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">fprint_seq_digest_md5</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="374" style="width: 35px; color: rgba(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="382" style="width: 35px; color: rgba(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">@@ -374,7 +382,7 @@ void fasta_print_general(FILE * fp,</td>
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374
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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;">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=%.4lf"</span><span class="p">,</span> <span class="n" style="color: #333;">score_name</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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375
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp"></span>
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376
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<td class="diff-line-num new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_relabel_keep</span> <span class="o" style="font-weight: 600;">&&</span></span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="cpp"> <span class="p">((</span><span class="n" style="color: #333;">opt_relabel</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ordinal</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_sha1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_md5</span><span class="p">))</span></span>
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<td class="diff-line-num new old_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); 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="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="p">((</span><span class="n" style="color: #333;">opt_relabel</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ordinal</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_sha1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_md5</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 right">opt_relabel_self</span></span><span class="p">))</span></span>
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378
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<td class="diff-line-num new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
386
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<pre style="margin: 0;"> <span id="LC386" 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;">header</span><span class="p">);</span></span>
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379
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"></span>
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380
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<td class="diff-line-num 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">
388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/commit/a6e84605ff4ae3d2eb2fe51571bda5469e368a1e#dce607e2c5a20b2277b76421039058016c3f2150"><strong>src/fasta.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,7 +91,7 @@ void fasta_print_general(FILE * fp,</td>
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91
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">,</span></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="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">header</span><span class="p">,</span></span>
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93
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">header_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">abundance</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ordinal</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ee</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">clustersize</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">@@ -446,6 +446,12 @@ int64_t fastq_get_abundance_and_presence(fastx_handle h)</td>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">header_get_size</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;">header_buffer</span><span class="p">.</span><span class="n" style="color: #333;">data</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;">header_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="LC447" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">fprint_seq_label</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span> <span 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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* normalize first? */</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"%.*s"</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">fastq_print_general</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC456" 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="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</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">@@ -458,7 +464,9 @@ void fastq_print_general(FILE * fp,</td>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"@"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_relabel_sha1</span><span class="p">)</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_relabel_self</span><span class="p">)</span></span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"> <span class="n" style="color: #333;">fprint_seq_label</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" 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_relabel_sha1</span><span class="p">)</span></span>
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462
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470
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="cpp"> <span class="n" style="color: #333;">fprint_seq_digest_sha1</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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463
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471
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<pre style="margin: 0;"> <span id="LC471" 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_relabel_md5</span><span class="p">)</span></span>
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464
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472
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp"> <span class="n" style="color: #333;">fprint_seq_digest_md5</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="482" style="width: 35px; color: rgba(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="490" style="width: 35px; color: rgba(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">@@ -482,7 +490,7 @@ void fastq_print_general(FILE * fp,</td>
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482
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490
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<pre style="margin: 0;"> <span id="LC490" 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;">";ee=%.4lf"</span><span class="p">,</span> <span class="n" style="color: #333;">ee</span><span class="p">);</span></span>
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483
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491
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="cpp"></span>
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484
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_relabel_keep</span> <span class="o" style="font-weight: 600;">&&</span></span>
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485
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="cpp"> <span class="p">((</span><span class="n" style="color: #333;">opt_relabel</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ordinal</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_sha1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_md5</span><span class="p">))</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp"> <span class="p">((</span><span class="n" style="color: #333;">opt_relabel</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ordinal</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_sha1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt_relabel_md5</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 right">opt_relabel_self</span></span><span class="p">))</span></span>
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486
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494
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">" %.*s"</span><span class="p">,</span> <span class="n" style="color: #333;">header_len</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">);</span></span>
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487
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495
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cpp"></span>
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488
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496
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%.*s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%.*s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">quality</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/commit/a6e84605ff4ae3d2eb2fe51571bda5469e368a1e#5158e97b06e3c2eb531bf6a179b392990120db5a"><strong>src/filter.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="433" style="width: 35px; color: rgba(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="433" style="width: 35px; color: rgba(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">@@ -433,7 +433,7 @@ void filter(bool fastq_only, char * filename)</td>
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433
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433
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastaout_rev</span><span class="p">)</span></span>
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434
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434
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">fasta_print_general</span><span class="p">(</span><span class="n" style="color: #333;">fp_fastaout_rev</span><span class="p">,</span></span>
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435
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435
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="cpp"> <span class="n" style="color: #333;">fastx_get_sequence</span><span class="p">(</span><span class="n" style="color: #333;">h<span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">res2</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp"> <span class="n" style="color: #333;">fastx_get_sequence</span><span class="p">(</span><span class="n" style="color: #333;">h<span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">res2</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="cpp"> <span class="n" style="color: #333;">res2</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="LC438" class="line" lang="cpp"> <span class="n" style="color: #333;">fastx_get_header</span><span class="p">(</span><span class="n" style="color: #333;">h2</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="cpp"> <span class="n" style="color: #333;">fastx_get_header_length</span><span class="p">(</span><span class="n" style="color: #333;">h2</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">@@ -1408,7 +1408,7 @@ void fastq_mergepairs()</td>
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<pre style="margin: 0;"> <span id="LC1408" class="line" lang="cpp"></span>
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1409
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<pre style="margin: 0;"> <span id="LC1409" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failed_minscore</span><span class="p">)</span></span>
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1410
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<pre style="margin: 0;"> <span id="LC1410" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1411" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" alignment score too low, or score drop to high</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="cpp"> <span class="s" style="color: #d14;">"%10"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" alignment score too low, or score drop to<span class="idiff left right">o</span> high</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1412" class="line" lang="cpp"> <span class="n" style="color: #333;">failed_minscore</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">failed_minovlen</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">@@ -296,7 +296,7 @@ void msa(FILE * fp_msaout, FILE * fp_consout, FILE * fp_profile,</td>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">best_count</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"> <span class="n" style="color: #333;">best_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">best_sym</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">best_sym</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">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="n" style="color: #333;"><span class="idiff right">c</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/vsearch/commit/a6e84605ff4ae3d2eb2fe51571bda5469e368a1e#d6b1377ec11c4f9379910db0cc295c16f7dbf5e2"><strong>src/sffconvert.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">@@ -335,7 +335,7 @@ void sff_convert()</td>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;">read_name</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">read_name</span><span class="p">),</span></span>
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337
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337
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">clip_start</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">,</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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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">read_no</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 right">1</span></span><span class="p">,</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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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">read_name</span><span class="p">);</span></span>
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">xfree</span><span class="p">(</span><span class="n" style="color: #333;">bases</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/vsearch/commit/a6e84605ff4ae3d2eb2fe51571bda5469e368a1e#b0109d980457466d1deec0f79c45e2b54114fdd5"><strong>src/vsearch.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,6 +76,7 @@ bool opt_no_progress;</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">opt_quiet</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">opt_relabel_keep</span><span class="p">;</span></span>
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">opt_relabel_md5</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">opt_relabel_self</span><span class="p">;</span></span>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">opt_relabel_sha1</span><span class="p">;</span></span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">opt_samheader</span><span class="p">;</span></span>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">opt_sff_clip</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">@@ -826,6 +827,7 @@ void args_init(int argc, char **argv)</td>
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826
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_relabel</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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827
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_relabel_keep</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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828
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_relabel_md5</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="LC830" 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;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_relabel_sha1</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="LC832" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_rereplicate</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="LC833" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_reverse</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -884,456 +886,458 @@ void args_init(int argc, char **argv)</td>
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886
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="cpp"></span>
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887
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">enum</span></span>
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888
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC887" class="line" lang="cpp"> <span class="n" style="color: #333;">option_help</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC888" class="line" lang="cpp"> <span class="n" style="color: #333;">option_version</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="cpp"> <span class="n" style="color: #333;">option_abskew</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="cpp"> <span class="n" style="color: #333;">option_acceptall</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="cpp"> <span class="n" style="color: #333;">option_alignwidth</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="cpp"> <span class="n" style="color: #333;">option_allpairs_global</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC893" class="line" lang="cpp"> <span class="n" style="color: #333;">option_alnout</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC890" class="line" lang="cpp"> <span class="n" style="color: #333;">option_usearch_global</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC891" class="line" lang="cpp"> <span class="n" style="color: #333;">option_db</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC892" class="line" lang="cpp"> <span class="n" style="color: #333;">option_id</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC893" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxaccepts</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC894" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxrejects</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC896" class="line" lang="cpp"> <span class="n" style="color: #333;">option_match</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC897" class="line" lang="cpp"> <span class="n" style="color: #333;">option_mismatch</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC898" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fulldp</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC899" class="line" lang="cpp"> <span class="n" style="color: #333;">option_strand</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC900" class="line" lang="cpp"> <span class="n" style="color: #333;">option_threads</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC901" class="line" lang="cpp"> <span class="n" style="color: #333;">option_gapopen</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC902" class="line" lang="cpp"> <span class="n" style="color: #333;">option_gapext</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC903" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rowlen</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC904" class="line" lang="cpp"> <span class="n" style="color: #333;">option_userfields</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC905" class="line" lang="cpp"> <span class="n" style="color: #333;">option_userout</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC906" class="line" lang="cpp"> <span class="n" style="color: #333;">option_self</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="cpp"> <span class="n" style="color: #333;">option_band</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="cpp"> <span class="n" style="color: #333;">option_biomout</span><span class="p">,</span></span>
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896
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<pre style="margin: 0;"> <span id="LC896" class="line" lang="cpp"> <span class="n" style="color: #333;">option_blast6out</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC908" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uc</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC909" class="line" lang="cpp"> <span class="n" style="color: #333;">option_weak_id</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC910" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uc_allhits</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC911" class="line" lang="cpp"> <span class="n" style="color: #333;">option_notrunclabels</span><span class="p">,</span></span>
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912
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<pre style="margin: 0;">-<span id="LC912" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sortbysize</span><span class="p">,</span></span>
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913
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<pre style="margin: 0;">-<span id="LC913" class="line" lang="cpp"> <span class="n" style="color: #333;">option_output</span><span class="p">,</span></span>
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914
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<pre style="margin: 0;">-<span id="LC914" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minsize</span><span class="p">,</span></span>
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915
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<pre style="margin: 0;">-<span id="LC915" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxsize</span><span class="p">,</span></span>
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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_relabel</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
917
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<pre style="margin: 0;">-<span id="LC917" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
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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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919
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<pre style="margin: 0;">-<span id="LC919" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minseqlength</span><span class="p">,</span></span>
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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_minuniquesize</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
921
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<pre style="margin: 0;">-<span id="LC921" class="line" lang="cpp"> <span class="n" style="color: #333;">option_topn</span><span class="p">,</span></span>
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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_maxseqlength</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
923
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC923" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
924
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC924" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sortbylength</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
925
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC925" class="line" lang="cpp"> <span class="n" style="color: #333;">option_matched</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
926
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC926" class="line" lang="cpp"> <span class="n" style="color: #333;">option_notmatched</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
927
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC927" class="line" lang="cpp"> <span class="n" style="color: #333;">option_dbmatched</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
928
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC928" class="line" lang="cpp"> <span class="n" style="color: #333;">option_dbnotmatched</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
929
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC929" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastapairs</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
930
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC930" class="line" lang="cpp"> <span class="n" style="color: #333;">option_output_no_hits</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" 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">
931
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC931" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxhits</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
932
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(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="LC932" class="line" lang="cpp"> <span class="n" style="color: #333;">option_top_hits_only</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
933
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(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="LC933" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fasta_width</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
934
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(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="LC934" class="line" lang="cpp"> <span class="n" style="color: #333;">option_query_cov</span><span class="p">,</span></span>
</pre>
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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="897" style="width: 35px; color: rgba(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="LC935" class="line" lang="cpp"> <span class="n" style="color: #333;">option_target_cov</span><span class="p">,</span></span>
</pre>
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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="897" style="width: 35px; color: rgba(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="LC936" class="line" lang="cpp"> <span class="n" style="color: #333;">option_idprefix</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
937
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC937" class="line" lang="cpp"> <span class="n" style="color: #333;">option_idsuffix</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
938
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC938" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minqt</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
939
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC939" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxqt</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
940
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC940" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minsl</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
941
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC941" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxsl</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
942
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC942" class="line" lang="cpp"> <span class="n" style="color: #333;">option_leftjust</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
943
</td>
<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC943" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rightjust</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
944
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC944" class="line" lang="cpp"> <span class="n" style="color: #333;">option_selfid</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
945
</td>
<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC945" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxid</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
946
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<td class="diff-line-num new_line old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC946" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minsizeratio</span><span class="p">,</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC947" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxsizeratio</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC948" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxdiffs</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC949" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxsubs</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC950" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxgaps</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC951" class="line" lang="cpp"> <span class="n" style="color: #333;">option_mincols</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC952" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxqsize</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC953" class="line" lang="cpp"> <span class="n" style="color: #333;">option_mintsize</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC954" class="line" lang="cpp"> <span class="n" style="color: #333;">option_mid</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC955" class="line" lang="cpp"> <span class="n" style="color: #333;">option_shuffle</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC956" class="line" lang="cpp"> <span class="n" style="color: #333;">option_randseed</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC957" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maskfasta</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC958" class="line" lang="cpp"> <span class="n" style="color: #333;">option_hardmask</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC959" class="line" lang="cpp"> <span class="n" style="color: #333;">option_qmask</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC960" class="line" lang="cpp"> <span class="n" style="color: #333;">option_dbmask</span><span class="p">,</span></span>
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961
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<pre style="margin: 0;">-<span id="LC961" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cluster_smallmem</span><span class="p">,</span></span>
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962
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<pre style="margin: 0;">-<span id="LC962" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cluster_fast</span><span class="p">,</span></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="cpp"> <span class="n" style="color: #333;">option_borderline</span><span class="p">,</span></span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="cpp"> <span class="n" style="color: #333;">option_bzip2_decompress</span><span class="p">,</span></span>
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963
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899
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="cpp"> <span class="n" style="color: #333;">option_centroids</span><span class="p">,</span></span>
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964
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<pre style="margin: 0;">-<span id="LC964" class="line" lang="cpp"> <span class="n" style="color: #333;">option_clusters</span><span class="p">,</span></span>
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965
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<pre style="margin: 0;">-<span id="LC965" class="line" lang="cpp"> <span class="n" style="color: #333;">option_consout</span><span class="p">,</span></span>
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966
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<pre style="margin: 0;">-<span id="LC966" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cons_truncate</span><span class="p">,</span></span>
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967
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<pre style="margin: 0;">-<span id="LC967" class="line" lang="cpp"> <span class="n" style="color: #333;">option_msaout</span><span class="p">,</span></span>
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968
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<pre style="margin: 0;">-<span id="LC968" class="line" lang="cpp"> <span class="n" style="color: #333;">option_usersort</span><span class="p">,</span></span>
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969
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<pre style="margin: 0;">-<span id="LC969" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xn</span><span class="p">,</span></span>
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970
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<pre style="margin: 0;">-<span id="LC970" class="line" lang="cpp"> <span class="n" style="color: #333;">option_iddef</span><span class="p">,</span></span>
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971
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<pre style="margin: 0;">-<span id="LC971" class="line" lang="cpp"> <span class="n" style="color: #333;">option_slots</span><span class="p">,</span></span>
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972
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<pre style="margin: 0;">-<span id="LC972" class="line" lang="cpp"> <span class="n" style="color: #333;">option_pattern</span><span class="p">,</span></span>
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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;">option_maxuniquesize</span><span class="p">,</span></span>
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974
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<pre style="margin: 0;">-<span id="LC974" class="line" lang="cpp"> <span class="n" style="color: #333;">option_abskew</span><span class="p">,</span></span>
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975
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900
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="cpp"> <span class="n" style="color: #333;">option_chimeras</span><span class="p">,</span></span>
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976
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<pre style="margin: 0;">-<span id="LC976" class="line" lang="cpp"> <span class="n" style="color: #333;">option_dn</span><span class="p">,</span></span>
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977
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<td class="diff-line-num new_line old" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC977" class="line" lang="cpp"> <span class="n" style="color: #333;">option_mindiffs</span><span class="p">,</span></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;">option_mindiv</span><span class="p">,</span></span>
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979
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<pre style="margin: 0;">-<span id="LC979" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minh</span><span class="p">,</span></span>
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980
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<pre style="margin: 0;">-<span id="LC980" class="line" lang="cpp"> <span class="n" style="color: #333;">option_nonchimeras</span><span class="p">,</span></span>
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981
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<pre style="margin: 0;">-<span id="LC981" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uchime_denovo</span><span class="p">,</span></span>
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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;">option_uchime_ref</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 class="n" style="color: #333;">option_uchimealns</span><span class="p">,</span></span>
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984
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<pre style="margin: 0;">-<span id="LC984" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uchimeout</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="n" style="color: #333;">option_uchimeout5</span><span class="p">,</span></span>
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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;">option_alignwidth</span><span class="p">,</span></span>
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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;">option_allpairs_global</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC988" class="line" lang="cpp"> <span class="n" style="color: #333;">option_acceptall</span><span class="p">,</span></span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cluster_fast</span><span class="p">,</span></span>
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989
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902
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cluster_size</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC990" class="line" lang="cpp"> <span class="n" style="color: #333;">option_samout</span><span class="p">,</span></span>
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991
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<pre style="margin: 0;">-<span id="LC991" class="line" lang="cpp"> <span class="n" style="color: #333;">option_log</span><span class="p">,</span></span>
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992
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<pre style="margin: 0;">-<span id="LC992" class="line" lang="cpp"> <span class="n" style="color: #333;">option_quiet</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC993" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastx_subsample</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC994" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sample_pct</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC995" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_chars</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC996" class="line" lang="cpp"> <span class="n" style="color: #333;">option_profile</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC997" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sample_size</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC998" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastaout</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC999" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span><span class="p">,</span></span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cluster_smallmem</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cluster_unoise</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC905" class="line" lang="cpp"> <span class="n" style="color: #333;">option_clusterout_id</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC906" class="line" lang="cpp"> <span class="n" style="color: #333;">option_clusterout_sort</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="cpp"> <span class="n" style="color: #333;">option_borderline</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1003" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1004" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="cpp"> <span class="n" style="color: #333;">option_clusters</span><span class="p">,</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cons_truncate</span><span class="p">,</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="cpp"> <span class="n" style="color: #333;">option_consout</span><span class="p">,</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cut</span><span class="p">,</span></span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cut_pattern</span><span class="p">,</span></span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="cpp"> <span class="n" style="color: #333;">option_db</span><span class="p">,</span></span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="cpp"> <span class="n" style="color: #333;">option_dbmask</span><span class="p">,</span></span>
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914
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<pre style="margin: 0;">+<span id="LC914" 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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<pre style="margin: 0;">+<span id="LC915" 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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<pre style="margin: 0;">+<span id="LC916" class="line" lang="cpp"> <span class="n" style="color: #333;">option_derep_fulllength</span><span class="p">,</span></span>
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1005
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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_derep_prefix</span><span class="p">,</span></span>
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1006
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<pre style="margin: 0;">-<span id="LC1006" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_filter</span><span class="p">,</span></span>
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1007
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<pre style="margin: 0;">-<span id="LC1007" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastqout</span><span class="p">,</span></span>
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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_dn</span><span class="p">,</span></span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="cpp"> <span class="n" style="color: #333;">option_ee_cutoffs</span><span class="p">,</span></span>
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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_eeout</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="cpp"> <span class="n" style="color: #333;">option_eetabbedout</span><span class="p">,</span></span>
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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_fasta_score</span><span class="p">,</span></span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fasta_width</span><span class="p">,</span></span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastaout</span><span class="p">,</span></span>
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1008
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925
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastaout_discarded</span><span class="p">,</span></span>
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1009
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<td class="diff-line-num new_line old" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1009" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastqout_discarded</span><span class="p">,</span></span>
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1010
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<pre style="margin: 0;">-<span id="LC1010" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_truncqual</span><span class="p">,</span></span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastaout_discarded_rev</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastaout_notmerged_fwd</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastaout_notmerged_rev</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastaout_rev</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastapairs</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_allowmergestagger</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_ascii</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_asciiout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_chars</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); 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="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_convert</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); 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="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_eeout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); 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="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_eestats</span><span class="p">,</span></span>
</pre>
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938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_eestats2</span><span class="p">,</span></span>
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939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_filter</span><span class="p">,</span></span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_join</span><span class="p">,</span></span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_maxdiffpct</span><span class="p">,</span></span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_maxdiffs</span><span class="p">,</span></span>
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1011
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943
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<pre style="margin: 0;"> <span id="LC943" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_maxee</span><span class="p">,</span></span>
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1012
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<pre style="margin: 0;">-<span id="LC1012" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_trunclen</span><span class="p">,</span></span>
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1013
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<pre style="margin: 0;">-<span id="LC1013" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_minlen</span><span class="p">,</span></span>
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1014
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<pre style="margin: 0;">-<span id="LC1014" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_stripleft</span><span class="p">,</span></span>
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1015
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944
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<pre style="margin: 0;"> <span id="LC944" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_maxee_rate</span><span class="p">,</span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_maxlen</span><span class="p">,</span></span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_maxmergelen</span><span class="p">,</span></span>
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1016
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947
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<pre style="margin: 0;"> <span id="LC947" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_maxns</span><span class="p">,</span></span>
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1017
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<pre style="margin: 0;">-<span id="LC1017" class="line" lang="cpp"> <span class="n" style="color: #333;">option_eeout</span><span class="p">,</span></span>
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1018
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<pre style="margin: 0;">-<span id="LC1018" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_ascii</span><span class="p">,</span></span>
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1019
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<td class="diff-line-num new_line old" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1019" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_qmin</span><span class="p">,</span></span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_mergepairs</span><span class="p">,</span></span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_minlen</span><span class="p">,</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_minmergelen</span><span class="p">,</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_minovlen</span><span class="p">,</span></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_nostagger</span><span class="p">,</span></span>
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1020
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953
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<pre style="margin: 0;"> <span id="LC953" 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="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="954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
954
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<pre style="margin: 0;"> <span id="LC954" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_qmaxout</span><span class="p">,</span></span>
</pre>
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955
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<pre style="margin: 0;">+<span id="LC955" 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 new_line" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_qminout</span><span class="p">,</span></span>
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1022
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<td class="diff-line-num new_line" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
957
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_stats</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); 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="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_stripleft</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); 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="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_stripright</span><span class="p">,</span></span>
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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="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
960
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC960" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_tail</span><span class="p">,</span></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="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1024" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastx_revcomp</span><span class="p">,</span></span>
</pre>
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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
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1025" class="line" lang="cpp"> <span class="n" style="color: #333;">option_label_suffix</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1026
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1026" class="line" lang="cpp"> <span class="n" style="color: #333;">option_h</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1027
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1027" class="line" lang="cpp"> <span class="n" style="color: #333;">option_samheader</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1028
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1028" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeorder</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1029
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1029" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minwordmatches</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1030
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1030" class="line" lang="cpp"> <span class="n" style="color: #333;">option_v</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1031
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1031" 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 old old_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1032
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1032" class="line" lang="cpp"> <span class="n" style="color: #333;">option_search_exact</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1033
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1033" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastx_mask</span><span class="p">,</span></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="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1034
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1034" class="line" lang="cpp"> <span class="n" style="color: #333;">option_min_unmasked_pct</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1035
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1035" class="line" lang="cpp"> <span class="n" style="color: #333;">option_max_unmasked_pct</span><span class="p">,</span></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="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1036
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1036" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_convert</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1037
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1037" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_asciiout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1038
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1038" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_qminout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1039
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1039" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_mergepairs</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1040
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1040" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_eeout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1041
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1041" 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 old old_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1042
</td>
<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1042" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastqout_notmerged_rev</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1043
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<pre style="margin: 0;">-<span id="LC1043" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_minovlen</span><span class="p">,</span></span>
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1044
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1044" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_minmergelen</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1045
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1045" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_maxmergelen</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1046
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1046" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_nostagger</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1047
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1047" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_allowmergestagger</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" 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">
1048
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1048" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_maxdiffs</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1049
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1049" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastaout_notmerged_fwd</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1050
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1050" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastaout_notmerged_rev</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1051
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1051" class="line" lang="cpp"> <span class="n" style="color: #333;">option_reverse</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1052
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1052" class="line" lang="cpp"> <span class="n" style="color: #333;">option_eetabbedout</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1053
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1053" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fasta_score</span><span class="p">,</span></span>
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1054
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1054" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_eestats</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1055
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1055" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rereplicate</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1056
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<pre style="margin: 0;">-<span id="LC1056" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xdrop_nw</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1057
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1057" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minhsp</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1058
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1058" class="line" lang="cpp"> <span class="n" style="color: #333;">option_band</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1059
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1059" class="line" lang="cpp"> <span class="n" style="color: #333;">option_hspw</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1060
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1060" 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 old old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1061
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1061" 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 old_line" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1062
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<td class="diff-line-num new_line old" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1062" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_maxlen</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1063
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<td class="diff-line-num new_line" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_truncee</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1064
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<td class="diff-line-num new_line old" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1064" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastx_filter</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1065
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<td class="diff-line-num new_line old" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1065" class="line" lang="cpp"> <span class="n" style="color: #333;">option_otutabout</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1066
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<td class="diff-line-num new_line old" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1066" class="line" lang="cpp"> <span class="n" style="color: #333;">option_mothur_shared_out</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1067
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<pre style="margin: 0;">-<span id="LC1067" class="line" lang="cpp"> <span class="n" style="color: #333;">option_biomout</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_trunclen</span><span class="p">,</span></span>
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1068
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<td class="diff-line-num new_line" data-linenumber="963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
963
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_trunclen_keep</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1069
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1069" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_stripright</span><span class="p">,</span></span>
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1070
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="cpp"> <span class="n" style="color: #333;">option_no_progress</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1071
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1071" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_eestats2</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1072
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1072" 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 old old_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1073
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1073" class="line" lang="cpp"> <span class="n" style="color: #333;">option_length_cutoffs</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1074
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1074" class="line" lang="cpp"> <span class="n" style="color: #333;">option_makeudb_usearch</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1075
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1075" class="line" lang="cpp"> <span class="n" style="color: #333;">option_udb2fasta</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1076
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1076" class="line" lang="cpp"> <span class="n" style="color: #333;">option_udbinfo</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1077
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1077" class="line" lang="cpp"> <span class="n" style="color: #333;">option_udbstats</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1078
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1078" 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 old_line" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1079
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1079" class="line" lang="cpp"> <span class="n" style="color: #333;">option_unoise_alpha</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1080
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1080" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uchime2_denovo</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1081
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1081" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uchime3_denovo</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1082
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1082" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sintax</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1083
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1083" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sintax_cutoff</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1084
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(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="LC1084" class="line" lang="cpp"> <span class="n" style="color: #333;">option_tabbedout</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1085
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1085" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_maxdiffpct</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1086
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1086" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_join</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1087
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1087" class="line" lang="cpp"> <span class="n" style="color: #333;">option_join_padgap</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1088
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1088" class="line" lang="cpp"> <span class="n" style="color: #333;">option_join_padgapq</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1089
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(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="LC1089" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sff_convert</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1090
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(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="LC1090" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sff_clip</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1091" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastaout_rev</span><span class="p">,</span></span>
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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;">option_fastaout_discarded_rev</span><span class="p">,</span></span>
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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;">option_fastqout_rev</span><span class="p">,</span></span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_truncqual</span><span class="p">,</span></span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastqout</span><span class="p">,</span></span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastqout_discarded</span><span class="p">,</span></span>
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1094
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastqout_discarded_rev</span><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 class="n" style="color: #333;">option_xee</span><span class="p">,</span></span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastqout_notmerged_fwd</span><span class="p">,</span></span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastqout_notmerged_rev</span><span class="p">,</span></span>
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970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastqout_rev</span><span class="p">,</span></span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastx_filter</span><span class="p">,</span></span>
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1096
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972
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<pre style="margin: 0;"> <span id="LC972" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastx_getseq</span><span class="p">,</span></span>
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1097
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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;">option_fastx_getseqs</span><span class="p">,</span></span>
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1098
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974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastx_getsubseq</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="n" style="color: #333;">option_label_substr_match</span><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 class="n" style="color: #333;">option_label</span><span class="p">,</span></span>
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1101
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<pre style="margin: 0;">-<span id="LC1101" class="line" lang="cpp"> <span class="n" style="color: #333;">option_subseq_start</span><span class="p">,</span></span>
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1102
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<pre style="margin: 0;">-<span id="LC1102" class="line" lang="cpp"> <span class="n" style="color: #333;">option_subseq_end</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1103
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<pre style="margin: 0;">-<span id="LC1103" class="line" lang="cpp"> <span class="n" style="color: #333;">option_notmatchedfq</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastx_mask</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastx_revcomp</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastx_subsample</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fulldp</span><span class="p">,</span></span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="cpp"> <span class="n" style="color: #333;">option_gapext</span><span class="p">,</span></span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="cpp"> <span class="n" style="color: #333;">option_gapopen</span><span class="p">,</span></span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="cpp"> <span class="n" style="color: #333;">option_gzip_decompress</span><span class="p">,</span></span>
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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;">option_h</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 class="n" style="color: #333;">option_hardmask</span><span class="p">,</span></span>
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984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="cpp"> <span class="n" style="color: #333;">option_help</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="n" style="color: #333;">option_hspw</span><span class="p">,</span></span>
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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;">option_id</span><span class="p">,</span></span>
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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;">option_iddef</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;">option_idprefix</span><span class="p">,</span></span>
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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="cpp"> <span class="n" style="color: #333;">option_idsuffix</span><span class="p">,</span></span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="cpp"> <span class="n" style="color: #333;">option_join_padgap</span><span class="p">,</span></span>
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991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="cpp"> <span class="n" style="color: #333;">option_join_padgapq</span><span class="p">,</span></span>
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992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="cpp"> <span class="n" style="color: #333;">option_label</span><span class="p">,</span></span>
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1104
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993
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<pre style="margin: 0;"> <span id="LC993" class="line" lang="cpp"> <span class="n" style="color: #333;">option_label_field</span><span class="p">,</span></span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="cpp"> <span class="n" style="color: #333;">option_label_substr_match</span><span class="p">,</span></span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="cpp"> <span class="n" style="color: #333;">option_label_suffix</span><span class="p">,</span></span>
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1105
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996
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<pre style="margin: 0;"> <span id="LC996" class="line" lang="cpp"> <span class="n" style="color: #333;">option_label_word</span><span class="p">,</span></span>
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1106
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997
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<pre style="margin: 0;"> <span id="LC997" class="line" lang="cpp"> <span class="n" style="color: #333;">option_label_words</span><span class="p">,</span></span>
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1107
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998
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<pre style="margin: 0;"> <span id="LC998" class="line" lang="cpp"> <span class="n" style="color: #333;">option_labels</span><span class="p">,</span></span>
</pre>
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1108
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<pre style="margin: 0;">-<span id="LC1108" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cut</span><span class="p">,</span></span>
</pre>
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1109
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<td class="diff-line-num new_line old" data-linenumber="999" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1109" class="line" lang="cpp"> <span class="n" style="color: #333;">option_cut_pattern</span></span>
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999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="cpp"> <span class="n" style="color: #333;">option_leftjust</span><span class="p">,</span></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;">option_length_cutoffs</span><span class="p">,</span></span>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="cpp"> <span class="n" style="color: #333;">option_log</span><span class="p">,</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="cpp"> <span class="n" style="color: #333;">option_makeudb_usearch</span><span class="p">,</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maskfasta</span><span class="p">,</span></span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="cpp"> <span class="n" style="color: #333;">option_match</span><span class="p">,</span></span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="cpp"> <span class="n" style="color: #333;">option_matched</span><span class="p">,</span></span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="cpp"> <span class="n" style="color: #333;">option_max_unmasked_pct</span><span class="p">,</span></span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxaccepts</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxdiffs</span><span class="p">,</span></span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxgaps</span><span class="p">,</span></span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxhits</span><span class="p">,</span></span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxid</span><span class="p">,</span></span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxqsize</span><span class="p">,</span></span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxqt</span><span class="p">,</span></span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxrejects</span><span class="p">,</span></span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" 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="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="cpp"> <span class="n" style="color: #333;">option_maxsize</span><span class="p">,</span></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="cpp"> <span class="n" style="color: #333;">option_maxsizeratio</span><span class="p">,</span></span>
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1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxsl</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxsubs</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="cpp"> <span class="n" style="color: #333;">option_maxuniquesize</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="cpp"> <span class="n" style="color: #333;">option_mid</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="cpp"> <span class="n" style="color: #333;">option_min_unmasked_pct</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="cpp"> <span class="n" style="color: #333;">option_mincols</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="cpp"> <span class="n" style="color: #333;">option_mindiffs</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="cpp"> <span class="n" style="color: #333;">option_mindiv</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_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">
1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minh</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minhsp</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minqt</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minseqlength</span><span class="p">,</span></span>
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1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minsize</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minsizeratio</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1032
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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="LC1032" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minsl</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="cpp"> <span class="n" style="color: #333;">option_mintsize</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1034
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<pre style="margin: 0;">+<span id="LC1034" 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="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="cpp"> <span class="n" style="color: #333;">option_minwordmatches</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="cpp"> <span class="n" style="color: #333;">option_mismatch</span><span class="p">,</span></span>
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1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="cpp"> <span class="n" style="color: #333;">option_mothur_shared_out</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;">option_msaout</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="cpp"> <span class="n" style="color: #333;">option_no_progress</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="cpp"> <span class="n" style="color: #333;">option_nonchimeras</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="cpp"> <span class="n" style="color: #333;">option_notmatched</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="cpp"> <span class="n" style="color: #333;">option_notmatchedfq</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1043
</td>
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="cpp"> <span class="n" style="color: #333;">option_notrunclabels</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1044
</td>
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="cpp"> <span class="n" style="color: #333;">option_otutabout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1045
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1045" class="line" lang="cpp"> <span class="n" style="color: #333;">option_output</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1046
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1046" class="line" lang="cpp"> <span class="n" style="color: #333;">option_output_no_hits</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1047
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1047" class="line" lang="cpp"> <span class="n" style="color: #333;">option_pattern</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1048
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1048" class="line" lang="cpp"> <span class="n" style="color: #333;">option_profile</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1049" class="line" lang="cpp"> <span class="n" style="color: #333;">option_qmask</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="cpp"> <span class="n" style="color: #333;">option_query_cov</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="cpp"> <span class="n" style="color: #333;">option_quiet</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="cpp"> <span class="n" style="color: #333;">option_randseed</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1053
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<pre style="margin: 0;">+<span id="LC1053" 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="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1054
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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="LC1054" 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 old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1055
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1055" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1056
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1056" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1057
</td>
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rereplicate</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1059
</td>
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="cpp"> <span class="n" style="color: #333;">option_reverse</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1060
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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="LC1060" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rightjust</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rowlen</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="cpp"> <span class="n" style="color: #333;">option_samheader</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="cpp"> <span class="n" style="color: #333;">option_samout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sample_pct</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sample_size</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="cpp"> <span class="n" style="color: #333;">option_search_exact</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="cpp"> <span class="n" style="color: #333;">option_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1068
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1068" class="line" lang="cpp"> <span class="n" style="color: #333;">option_selfid</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1069
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1069" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sff_clip</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1070
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1070" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sff_convert</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1071
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1071" class="line" lang="cpp"> <span class="n" style="color: #333;">option_shuffle</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1072
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1072" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sintax</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1073
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1073" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sintax_cutoff</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeorder</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="cpp"> <span class="n" style="color: #333;">option_slots</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sortbylength</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sortbysize</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="cpp"> <span class="n" style="color: #333;">option_strand</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="cpp"> <span class="n" style="color: #333;">option_subseq_end</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="cpp"> <span class="n" style="color: #333;">option_subseq_start</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="cpp"> <span class="n" style="color: #333;">option_tabbedout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="cpp"> <span class="n" style="color: #333;">option_target_cov</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1085
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<pre style="margin: 0;">+<span id="LC1085" 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="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="cpp"> <span class="n" style="color: #333;">option_top_hits_only</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="cpp"> <span class="n" style="color: #333;">option_topn</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1088
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<pre style="margin: 0;">+<span id="LC1088" 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 old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uc_allhits</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1090
</td>
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uchime2_denovo</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1091
</td>
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uchime3_denovo</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); 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="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1092
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1092" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uchime_denovo</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1093
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1093" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uchime_ref</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1094
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1094" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uchimealns</span><span class="p">,</span></span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1095
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1095" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uchimeout</span><span class="p">,</span></span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1096
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1096" class="line" lang="cpp"> <span class="n" style="color: #333;">option_uchimeout5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1097
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1097" class="line" lang="cpp"> <span class="n" style="color: #333;">option_udb2fasta</span><span class="p">,</span></span>
</pre>
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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;">option_udbinfo</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="n" style="color: #333;">option_udbstats</span><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 class="n" style="color: #333;">option_unoise_alpha</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="cpp"> <span class="n" style="color: #333;">option_usearch_global</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1102
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="cpp"> <span class="n" style="color: #333;">option_userfields</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="cpp"> <span class="n" style="color: #333;">option_userout</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1104
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="cpp"> <span class="n" style="color: #333;">option_usersort</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="cpp"> <span class="n" style="color: #333;">option_v</span><span class="p">,</span></span>
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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="cpp"> <span class="n" style="color: #333;">option_version</span><span class="p">,</span></span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="cpp"> <span class="n" style="color: #333;">option_weak_id</span><span class="p">,</span></span>
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1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="cpp"> <span class="n" style="color: #333;">option_wordlength</span><span class="p">,</span></span>
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1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xdrop_nw</span><span class="p">,</span></span>
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1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xee</span><span class="p">,</span></span>
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1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xn</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span></span>
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1110
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1113
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<pre style="margin: 0;"> <span id="LC1113" class="line" lang="cpp"> <span class="p">};</span></span>
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1111
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<td class="diff-line-num new_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1114
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<pre style="margin: 0;"> <span id="LC1114" class="line" lang="cpp"></span>
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1112
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<td class="diff-line-num new_line" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1115
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">long_options</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1113
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="cpp"> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1114
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<td class="diff-line-num new_line old" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1114" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1115
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<td class="diff-line-num new_line old" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1115" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"version"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); 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="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"abskew"</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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); 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="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1118
</td>
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"acceptall"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"alignwidth"</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 new new_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"allpairs_global"</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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1116
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<td class="diff-line-num new_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"alnout"</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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1117
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<td class="diff-line-num new_line old" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1117" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"usearch_global"</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 new old_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); 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="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"band"</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 new old_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); 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="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"biomout"</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 new new_line" data-linenumber="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"blast6out"</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 new new_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"borderline"</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 new new_line" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"bzip2_decompress"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); 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="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1127
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"centroids"</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 new old_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); 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="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"chimeras"</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 new new_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cluster_fast"</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 new old_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); 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="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cluster_size"</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 new old_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); 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="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cluster_smallmem"</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 new old_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); 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="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1132
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cluster_unoise"</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 new old_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); 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="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"clusterout_id"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); 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="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"clusterout_sort"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); 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="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"clusters"</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 new new_line" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cons_truncate"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"consout"</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 new new_line" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cut"</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 new new_line" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cut_pattern"</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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1118
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1140
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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"db"</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 new new_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"dbmask"</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 new new_line" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1142
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<pre style="margin: 0;">+<span id="LC1142" 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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<td class="diff-line-num new new_line" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1143
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<pre style="margin: 0;">+<span id="LC1143" 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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<td class="diff-line-num new new_line" data-linenumber="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1144
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<pre style="margin: 0;">+<span id="LC1144" 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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<td class="diff-line-num new new_line" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">"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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<td class="diff-line-num new new_line" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">"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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<td class="diff-line-num new new_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">"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 new new_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">"eeout"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">"eetabbedout"</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 new new_line" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">"fasta_score"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">"fasta_width"</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 new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastaout"</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 new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastaout_discarded"</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 new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastaout_discarded_rev"</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 new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1155
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastaout_notmerged_fwd"</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 new new_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastaout_notmerged_rev"</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 new new_line" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastaout_rev"</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 new new_line" data-linenumber="1158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1158
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastapairs"</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 new new_line" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_allowmergestagger"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_ascii"</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 new new_line" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_asciiout"</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 new new_line" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_chars"</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 new new_line" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_convert"</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 new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_eeout"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1165
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<pre style="margin: 0;">+<span id="LC1165" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_eestats"</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 new new_line" data-linenumber="1166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1166
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<pre style="margin: 0;">+<span id="LC1166" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_eestats2"</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 new new_line" data-linenumber="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_filter"</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>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_join"</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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxdiffpct"</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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1170
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxdiffs"</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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1171
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<pre style="margin: 0;">+<span id="LC1171" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxee"</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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1172
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<pre style="margin: 0;">+<span id="LC1172" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxee_rate"</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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1173
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<pre style="margin: 0;">+<span id="LC1173" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxlen"</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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1174
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<pre style="margin: 0;">+<span id="LC1174" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxmergelen"</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>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxns"</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 new new_line" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_mergepairs"</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 new new_line" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1177
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<pre style="margin: 0;">+<span id="LC1177" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_minlen"</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 new new_line" data-linenumber="1178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_minmergelen"</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 new new_line" data-linenumber="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1179
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<pre style="margin: 0;">+<span id="LC1179" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_minovlen"</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 new new_line" data-linenumber="1180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1180
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<pre style="margin: 0;">+<span id="LC1180" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_nostagger"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_qmax"</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 new new_line" data-linenumber="1182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_qmaxout"</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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1183
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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_qmin"</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 new new_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1184
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<pre style="margin: 0;">+<span id="LC1184" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_qminout"</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 new new_line" data-linenumber="1185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1185
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<pre style="margin: 0;">+<span id="LC1185" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_stats"</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 new new_line" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_stripleft"</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 new new_line" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_stripright"</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 new new_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_tail"</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 new new_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1189
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_truncee"</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 new new_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_trunclen"</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 new new_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1191
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<pre style="margin: 0;">+<span id="LC1191" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_trunclen_keep"</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 new new_line" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1192
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<pre style="margin: 0;">+<span id="LC1192" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_truncqual"</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 new new_line" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1193
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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastqout"</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 new new_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1194
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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastqout_discarded"</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 new new_line" data-linenumber="1195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1195
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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastqout_discarded_rev"</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 new new_line" data-linenumber="1196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1196
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<pre style="margin: 0;">+<span id="LC1196" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastqout_notmerged_fwd"</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 new new_line" data-linenumber="1197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1197
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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastqout_notmerged_rev"</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 new new_line" data-linenumber="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1198
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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastqout_rev"</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 new new_line" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1199
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_filter"</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 new new_line" data-linenumber="1200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1200
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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_getseq"</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 new new_line" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1201
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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_getseqs"</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 new new_line" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1202
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<pre style="margin: 0;">+<span id="LC1202" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_getsubseq"</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 new new_line" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1203
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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_mask"</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 new new_line" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1204
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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_revcomp"</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 new new_line" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1205
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_subsample"</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 new new_line" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1206
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<pre style="margin: 0;">+<span id="LC1206" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fulldp"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1207
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"gapext"</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 new new_line" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1208
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"gapopen"</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 new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1209
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"gzip_decompress"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"h"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1211
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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"hardmask"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); 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="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1212
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1213
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"hspw"</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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1119
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<td class="diff-line-num new_line" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1214
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<pre style="margin: 0;"> <span id="LC1214" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"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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<td class="diff-line-num new new_line" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1215
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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"iddef"</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 new new_line" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1216
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"idprefix"</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 new new_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1217
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<pre style="margin: 0;">+<span id="LC1217" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"idsuffix"</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 new new_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1218
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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"join_padgap"</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 new new_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1219
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"join_padgapq"</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 new new_line" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1220
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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"label"</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 new new_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1221
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<pre style="margin: 0;">+<span id="LC1221" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"label_field"</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 new new_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1222
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<pre style="margin: 0;">+<span id="LC1222" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"label_substr_match"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1223
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<pre style="margin: 0;">+<span id="LC1223" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"label_suffix"</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 new new_line" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1224
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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"label_word"</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 new new_line" data-linenumber="1225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1225
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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"label_words"</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 new new_line" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1226
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<pre style="margin: 0;">+<span id="LC1226" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"labels"</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 new new_line" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1227
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<pre style="margin: 0;">+<span id="LC1227" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"leftjust"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1228
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<pre style="margin: 0;">+<span id="LC1228" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"length_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 new new_line" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1229
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<pre style="margin: 0;">+<span id="LC1229" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"log"</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 new new_line" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1230
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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"makeudb_usearch"</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 new new_line" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1231
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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maskfasta"</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 new new_line" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"match"</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 new new_line" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1233
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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"matched"</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 new new_line" data-linenumber="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1234
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"max_unmasked_pct"</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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1120
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<td class="diff-line-num new_line" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1235
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<pre style="margin: 0;"> <span id="LC1235" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxaccepts"</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 new new_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1236
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<pre style="margin: 0;">+<span id="LC1236" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxdiffs"</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 new new_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxgaps"</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 new new_line" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxhits"</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 new new_line" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxid"</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 new new_line" data-linenumber="1240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxqsize"</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 new new_line" data-linenumber="1241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxqt"</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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1121
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1242
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<pre style="margin: 0;"> <span id="LC1242" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxrejects"</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 old old_line" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1122
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1122" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"wordlength"</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 old old_line" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1123
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1123" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"match"</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 old old_line" data-linenumber="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1124
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1124" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mismatch"</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 old old_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1125
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1125" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fulldp"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1126
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1126" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"strand"</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 old old_line" data-linenumber="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1127
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1127" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"threads"</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 old old_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1128
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1128" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"gapopen"</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 old old_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1129
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1129" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"gapext"</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 old old_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1130
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<pre style="margin: 0;">-<span id="LC1130" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"rowlen"</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 old old_line" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1131
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1131" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"userfields"</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 old old_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1132
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1132" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"userout"</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 old old_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1133
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1133" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"self"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1134
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1134" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"blast6out"</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 old old_line" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1135
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1135" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uc"</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 old old_line" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1136
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1136" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"weak_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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<td class="diff-line-num old old_line" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1137
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1137" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uc_allhits"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1138
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<td class="diff-line-num new_line old" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1138" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"notrunclabels"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1139
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<pre style="margin: 0;">-<span id="LC1139" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sortbysize"</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 old old_line" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1140
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<pre style="margin: 0;">-<span id="LC1140" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"output"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1141
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<pre style="margin: 0;">-<span id="LC1141" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minsize"</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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1243
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxseqlength"</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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1142
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1244
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<pre style="margin: 0;"> <span id="LC1244" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxsize"</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 old old_line" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1143
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<pre style="margin: 0;">-<span id="LC1143" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"relabel"</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 old old_line" data-linenumber="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1144
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<pre style="margin: 0;">-<span id="LC1144" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sizeout"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1145
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<td class="diff-line-num new_line old" data-linenumber="1245" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1145" 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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<td class="diff-line-num new old_line" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1245
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<pre style="margin: 0;">+<span id="LC1245" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxsizeratio"</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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1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxsl"</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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1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxsubs"</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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1248
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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxuniquesize"</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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1249
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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mid"</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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1250
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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"min_unmasked_pct"</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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1251
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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mincols"</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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1252
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<pre style="margin: 0;">+<span id="LC1252" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mindiffs"</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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1253
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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mindiv"</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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1254
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<pre style="margin: 0;">+<span id="LC1254" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minh"</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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1255
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<pre style="margin: 0;">+<span id="LC1255" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minhsp"</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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1256
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<pre style="margin: 0;">+<span id="LC1256" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minqt"</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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1257
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<pre style="margin: 0;"> <span id="LC1257" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minseqlength"</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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1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minsize"</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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1259
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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minsizeratio"</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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1260
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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minsl"</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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1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mintsize"</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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1262
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<pre style="margin: 0;"> <span id="LC1262" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minuniquesize"</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;">"topn"</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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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;">"maxseqlength"</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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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;">"sizein"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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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;">"sortbylength"</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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1152
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<pre style="margin: 0;">-<span id="LC1152" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"matched"</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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1153
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<pre style="margin: 0;">-<span id="LC1153" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"notmatched"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1154
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<pre style="margin: 0;">-<span id="LC1154" 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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1155
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<pre style="margin: 0;">-<span id="LC1155" 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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1156
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<pre style="margin: 0;">-<span id="LC1156" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastapairs"</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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1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minwordmatches"</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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1264
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<pre style="margin: 0;">+<span id="LC1264" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mismatch"</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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1265
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<pre style="margin: 0;">+<span id="LC1265" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mothur_shared_out"</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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1266
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<pre style="margin: 0;">+<span id="LC1266" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"msaout"</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 new new_line" data-linenumber="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1267
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<pre style="margin: 0;">+<span id="LC1267" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"no_progress"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1268
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<pre style="margin: 0;">+<span id="LC1268" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"nonchimeras"</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 new new_line" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1269
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<pre style="margin: 0;">+<span id="LC1269" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"notmatched"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"notmatchedfq"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"notrunclabels"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"otutabout"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1273
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"output"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1157
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<td class="diff-line-num new_line" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1274
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<pre style="margin: 0;"> <span id="LC1274" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"output_no_hits"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1158
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<td class="diff-line-num new_line old" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1158" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left right">maxhits</span>"</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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1159
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<pre style="margin: 0;">-<span id="LC1159" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left">top_hits_only"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">no_argument</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </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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1160
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<td class="diff-line-num new_line old" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1160" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left">fasta_width"</span></span><span class="p"><span class="idiff right">,</span></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 new old_line" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); 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="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left right">pattern</span>"</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 new old_line" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); 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="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left">profile"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">required_argument</span></span><span class="p"><span class="idiff right">,</span></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 new new_line" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left">qmask"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </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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1161
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<td class="diff-line-num new_line" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1278
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<pre style="margin: 0;"> <span id="LC1278" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"query_cov"</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 old old_line" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1162
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<td class="diff-line-num new_line old" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1162" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"target_cov"</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 old old_line" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1163
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<td class="diff-line-num new_line old" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1163" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"idprefix"</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 old old_line" data-linenumber="1164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1164
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<td class="diff-line-num new_line old" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1164" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"idsuffix"</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 old old_line" data-linenumber="1165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1165
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<td class="diff-line-num new_line old" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1165" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minqt"</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 old old_line" data-linenumber="1166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1166
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<td class="diff-line-num new_line old" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1166" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxqt"</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 old old_line" data-linenumber="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1167
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<td class="diff-line-num new_line old" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1167" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minsl"</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 old old_line" data-linenumber="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1168
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<td class="diff-line-num new_line old" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1168" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxsl"</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 old old_line" data-linenumber="1169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1169
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<td class="diff-line-num new_line old" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1169" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"leftjust"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1170" style="width: 35px; color: rgba(0,0,0,0.3); 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="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"quiet"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1170" style="width: 35px; color: rgba(0,0,0,0.3); 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="1280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"randseed"</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 new new_line" data-linenumber="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1281
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"relabel"</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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1170" style="width: 35px; color: rgba(0,0,0,0.3); 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="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"relabel_keep"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"relabel_md5"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1284
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"relabel_self"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1285
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"relabel_sha1"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"rereplicate"</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 new new_line" data-linenumber="1287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"reverse"</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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1170
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<td class="diff-line-num new_line" data-linenumber="1288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1288
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<pre style="margin: 0;"> <span id="LC1288" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"rightjust"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1171" style="width: 35px; color: rgba(0,0,0,0.3); 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="1289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1289
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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"rowlen"</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 new old_line" data-linenumber="1171" style="width: 35px; color: rgba(0,0,0,0.3); 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="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1290
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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"samheader"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1291
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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"samout"</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 new new_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1292
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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sample_pct"</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 new new_line" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1293
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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sample_size"</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 new new_line" data-linenumber="1294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1294
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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"search_exact"</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 new new_line" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1295
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<pre style="margin: 0;">+<span id="LC1295" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"self"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1171
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1296
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<pre style="margin: 0;"> <span id="LC1296" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"selfid"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1172
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<td class="diff-line-num new_line old" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1172" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxid"</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 old old_line" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1173
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<td class="diff-line-num new_line old" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1173" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minsizeratio"</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 old old_line" data-linenumber="1174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1174
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<td class="diff-line-num new_line old" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1174" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxsizeratio"</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 old old_line" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1175
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<td class="diff-line-num new_line old" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1175" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxdiffs"</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 old old_line" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1176
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<td class="diff-line-num new_line old" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1176" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxsubs"</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 old old_line" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1177
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<td class="diff-line-num new_line old" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1177" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxgaps"</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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1178
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<pre style="margin: 0;">-<span id="LC1178" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mincols"</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 old old_line" data-linenumber="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1179
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<td class="diff-line-num new_line old" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1179" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxqsize"</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 old old_line" data-linenumber="1180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1180
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<td class="diff-line-num new_line old" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1180" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mintsize"</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 old old_line" data-linenumber="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1181
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<td class="diff-line-num new_line old" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1181" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mid"</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 new old_line" data-linenumber="1182" style="width: 35px; color: rgba(0,0,0,0.3); 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="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1297
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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sff_clip"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1182" style="width: 35px; color: rgba(0,0,0,0.3); 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="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1298
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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sff_convert"</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 old_line" data-linenumber="1182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1182
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<td class="diff-line-num new_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"shuffle"</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 old old_line" data-linenumber="1183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1183
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<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1183" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"randseed"</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 old old_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1184
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<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1184" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maskfasta"</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 old old_line" data-linenumber="1185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1185
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<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1185" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"hardmask"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1186
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<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1186" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"qmask"</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 old old_line" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1187
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<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1187" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"dbmask"</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 old old_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1188
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<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1188" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cluster_smallmem"</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 old old_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1189
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<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1189" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cluster_fast"</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 old old_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1190
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<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1190" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"centroids"</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 old old_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1191
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<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1191" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"clusters"</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 old old_line" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1192
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<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1192" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"consout"</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 old old_line" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1193
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<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1193" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cons_truncate"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1194
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<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1194" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"msaout"</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 old old_line" data-linenumber="1195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1195
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<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1195" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"usersort"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1196
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<pre style="margin: 0;">-<span id="LC1196" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"xn"</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 old old_line" data-linenumber="1197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1197
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<pre style="margin: 0;">-<span id="LC1197" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"iddef"</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 new old_line" data-linenumber="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sintax"</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 new new_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sintax_cutoff"</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 new new_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sizein"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1303
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<pre style="margin: 0;">+<span id="LC1303" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sizeorder"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1304
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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sizeout"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1198
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1305
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<pre style="margin: 0;"> <span id="LC1305" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"slots"</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 old old_line" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1199
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<pre style="margin: 0;">-<span id="LC1199" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"pattern"</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 old old_line" data-linenumber="1200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1200
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<pre style="margin: 0;">-<span id="LC1200" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"maxuniquesize"</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 old old_line" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1201
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<pre style="margin: 0;">-<span id="LC1201" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"abskew"</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 old old_line" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1202
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<pre style="margin: 0;">-<span id="LC1202" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"chimeras"</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 old old_line" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1203
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<pre style="margin: 0;">-<span id="LC1203" 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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<td class="diff-line-num old old_line" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1204
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<pre style="margin: 0;">-<span id="LC1204" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mindiffs"</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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1205
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<pre style="margin: 0;">-<span id="LC1205" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mindiv"</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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1206
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<pre style="margin: 0;">-<span id="LC1206" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minh"</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 old old_line" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1207
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<td class="diff-line-num new_line old" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1207" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"nonchimeras"</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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1306
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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sortbylength"</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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1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sortbysize"</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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1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"strand"</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 new new_line" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"subseq_end"</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 new new_line" data-linenumber="1310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"subseq_start"</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 new new_line" data-linenumber="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1311
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"tabbedout"</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 new new_line" data-linenumber="1312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1312
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<pre style="margin: 0;">+<span id="LC1312" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"target_cov"</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 new new_line" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1313
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<pre style="margin: 0;">+<span id="LC1313" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"threads"</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 new new_line" data-linenumber="1314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1314
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<pre style="margin: 0;">+<span id="LC1314" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"top_hits_only"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1315
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<pre style="margin: 0;">+<span id="LC1315" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"topn"</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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1316
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<pre style="margin: 0;">+<span id="LC1316" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uc"</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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1317
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<pre style="margin: 0;">+<span id="LC1317" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uc_allhits"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uchime2_denovo"</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 new new_line" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uchime3_denovo"</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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1208
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1320
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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uchime_denovo"</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 old_line" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1209
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<td class="diff-line-num new_line" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1321
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uchime_ref"</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 old_line" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1210
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1322
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<pre style="margin: 0;"> <span id="LC1322" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uchimealns"</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 old_line" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1211
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<td class="diff-line-num new_line" data-linenumber="1323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1323
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<pre style="margin: 0;"> <span id="LC1323" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uchimeout"</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 old_line" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1212
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<td class="diff-line-num new_line" data-linenumber="1324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1324
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uchimeout5"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1213
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1213" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"alignwidth"</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 old old_line" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1214
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<pre style="margin: 0;">-<span id="LC1214" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"allpairs_global"</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 old old_line" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1215
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1215" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"acceptall"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1216
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1216" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cluster_size"</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 old old_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1217
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1217" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"samout"</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 old old_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1218
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1218" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"log"</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 old old_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1219
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1219" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"quiet"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1220
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1220" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_subsample"</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 old old_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1221
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1221" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sample_pct"</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 old old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1222
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1222" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_chars"</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 old old_line" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1223
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1223" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"profile"</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 old old_line" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1224
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1224" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sample_size"</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 old old_line" data-linenumber="1225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1225
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1225" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastaout"</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 old old_line" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1226
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1226" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"xsize"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1227
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1227" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"clusterout_id"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1228
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1228" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"clusterout_sort"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1229
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1229" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"borderline"</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 old old_line" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1230
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1230" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"relabel_sha1"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1231
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1231" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"relabel_md5"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1232
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1232" 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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1233
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1233" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_filter"</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 old old_line" data-linenumber="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1234
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1234" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastqout"</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 old old_line" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1235
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1235" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastaout_discarded"</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 old old_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1236
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1236" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastqout_discarded"</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 old old_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1237
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1237" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_truncqual"</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 old old_line" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1238
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1238" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxee"</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 old old_line" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1239
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1239" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_trunclen"</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 old old_line" data-linenumber="1240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1240
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1240" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_minlen"</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 old old_line" data-linenumber="1241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1241
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1241" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_stripleft"</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 old old_line" data-linenumber="1242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1242
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1242" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxee_rate"</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 old old_line" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1243
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1243" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxns"</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 old old_line" data-linenumber="1244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1244
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1244" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"eeout"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1245
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1245" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_ascii"</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 old old_line" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1246
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1246" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_qmin"</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 old old_line" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1247
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1247" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_qmax"</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 old old_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1248
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1248" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_qmaxout"</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 old old_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1249
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1249" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_stats"</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 old old_line" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1250
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1250" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_tail"</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 old old_line" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1251
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1251" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_revcomp"</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 old old_line" data-linenumber="1252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1252
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1252" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"label_suffix"</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 old old_line" data-linenumber="1253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1253
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1253" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"h"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1254
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1254" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"samheader"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1255
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1255" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sizeorder"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1256
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1256" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minwordmatches"</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 old old_line" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1257
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1257" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"v"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1258
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1258" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"relabel_keep"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1259
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1259" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"search_exact"</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 old old_line" data-linenumber="1260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1260
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1260" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_mask"</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 old old_line" data-linenumber="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1261
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1261" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"min_unmasked_pct"</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 old old_line" data-linenumber="1262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1262
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1262" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"max_unmasked_pct"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1263
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1263" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_convert"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1264
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1264" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_asciiout"</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 old old_line" data-linenumber="1265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1265
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1265" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_qminout"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1266
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1266" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_mergepairs"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1267
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1267" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_eeout"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1268
</td>
<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1268" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastqout_notmerged_fwd"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1269
</td>
<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1269" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastqout_notmerged_rev"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1270
</td>
<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1270" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_minovlen"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1271
</td>
<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1271" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_minmergelen"</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 old old_line" data-linenumber="1272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1272
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1272" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxmergelen"</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 old old_line" data-linenumber="1273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1273
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1273" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_nostagger"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1274
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1274" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_allowmergestagger"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1275
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1275" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxdiffs"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1276
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1276" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastaout_notmerged_fwd"</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 old old_line" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1277
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1277" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastaout_notmerged_rev"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1278
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1278" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"reverse"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1279
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1279" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"eetabbedout"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1280
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1280" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fasta_score"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1281
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1281" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_eestats"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1282
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1282" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"rereplicate"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1283
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1283" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"xdrop_nw"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1284
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1284" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"minhsp"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1285
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1285" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"band"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1286
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1286" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"hspw"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1287
</td>
<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1287" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"gzip_decompress"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1288
</td>
<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1288" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"bzip2_decompress"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1289
</td>
<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1289" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxlen"</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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1290
</td>
<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1290" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_truncee"</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 old old_line" data-linenumber="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1291
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1291" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_filter"</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 old old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1292
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1292" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"otutabout"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1293
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1293" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"mothur_shared_out"</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 old old_line" data-linenumber="1294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1294
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1294" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"biomout"</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 old old_line" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1295
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1295" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_trunclen_keep"</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 old old_line" data-linenumber="1296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1296
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1296" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_stripright"</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 old old_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1297
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1297" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"no_progress"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1298
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1298" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_eestats2"</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 old old_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1299
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<td class="diff-line-num new_line old" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1299" 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 old old_line" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1300
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<pre style="margin: 0;">-<span id="LC1300" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"length_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 old old_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1301
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<pre style="margin: 0;">-<span id="LC1301" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"makeudb_usearch"</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 old_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1302
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<td class="diff-line-num new_line" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1325
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<pre style="margin: 0;"> <span id="LC1325" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"udb2fasta"</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 old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1303
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<td class="diff-line-num new_line" data-linenumber="1326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1326
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<pre style="margin: 0;"> <span id="LC1326" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"udbinfo"</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 old_line" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1304
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<td class="diff-line-num new_line" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1327
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<pre style="margin: 0;"> <span id="LC1327" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"udbstats"</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 old old_line" data-linenumber="1305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1305
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<td class="diff-line-num new_line old" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1305" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cluster_unoise"</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 old_line" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1306
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<td class="diff-line-num new_line" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1328
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<pre style="margin: 0;"> <span id="LC1328" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"unoise_alpha"</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 old old_line" data-linenumber="1307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1307
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1307" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uchime2_denovo"</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 old old_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1308
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1308" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"uchime3_denovo"</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 old old_line" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1309
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1309" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sintax"</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 old old_line" data-linenumber="1310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1310
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1310" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sintax_cutoff"</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 old old_line" data-linenumber="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1311
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1311" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"tabbedout"</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 old old_line" data-linenumber="1312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1312
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1312" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_maxdiffpct"</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 old old_line" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1313
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1313" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastq_join"</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 old old_line" data-linenumber="1314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1314
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1314" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"join_padgap"</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 old old_line" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1315
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1315" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"join_padgapq"</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 old old_line" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1316
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1316" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sff_convert"</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 old old_line" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1317
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1317" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sff_clip"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1318
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1318" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastaout_rev"</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 old old_line" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1319
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1319" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastaout_discarded_rev"</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 old old_line" data-linenumber="1320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1320
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1320" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastqout_rev"</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 old old_line" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1321
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<td class="diff-line-num new_line old" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1321" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastqout_discarded_rev"</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 new old_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); 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="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1329
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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"usearch_global"</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 new old_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); 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="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1330
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"userfields"</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 new old_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); 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="1331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"userout"</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 new old_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); 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="1332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"usersort"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); 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="1333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"v"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); 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="1334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"version"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); 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="1335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"weak_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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<td class="diff-line-num new old_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); 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="1336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"wordlength"</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 new old_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); 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="1337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"xdrop_nw"</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 old_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1322
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<td class="diff-line-num new_line" data-linenumber="1338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1338
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<pre style="margin: 0;"> <span id="LC1338" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"xee"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1323
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1323" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_getseq"</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 old old_line" data-linenumber="1324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1324
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1324" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_getseqs"</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 old old_line" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1325
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1325" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fastx_getsubseq"</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 old old_line" data-linenumber="1326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1326
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1326" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"label_substr_match"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1327
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1327" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"label"</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 old old_line" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1328
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1328" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"subseq_start"</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 old old_line" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1329
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1329" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"subseq_end"</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 old old_line" data-linenumber="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1330
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1330" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"notmatchedfq"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1331
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1331" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"label_field"</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 old old_line" data-linenumber="1332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1332
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1332" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"label_word"</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 old old_line" data-linenumber="1333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1333
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1333" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"label_words"</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 old old_line" data-linenumber="1334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1334
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1334" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"labels"</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 old old_line" data-linenumber="1335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1335
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1335" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cut"</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 old old_line" data-linenumber="1336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1336
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<td class="diff-line-num new_line old" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1336" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"cut_pattern"</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 new old_line" data-linenumber="1337" style="width: 35px; color: rgba(0,0,0,0.3); 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="1339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"xn"</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 new old_line" data-linenumber="1337" style="width: 35px; color: rgba(0,0,0,0.3); 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="1340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1340
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"xsize"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">},</span></span>
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1337
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1341
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<pre style="margin: 0;"> <span id="LC1341" class="line" lang="cpp"> <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 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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1338
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1342
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="cpp"> <span class="p">};</span></span>
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1339
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1343
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2279" style="width: 35px; color: rgba(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="2283" style="width: 35px; color: rgba(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">@@ -2279,6 +2283,10 @@ void args_init(int argc, char **argv)</td>
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2279
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2283
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<pre style="margin: 0;"> <span id="LC2283" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_cut_pattern</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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2280
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2284
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<pre style="margin: 0;"> <span id="LC2284" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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2281
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2285
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<pre style="margin: 0;"> <span id="LC2285" class="line" lang="cpp"></span>
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2286
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<pre style="margin: 0;">+<span id="LC2286" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <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="2287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2287
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<pre style="margin: 0;">+<span id="LC2287" 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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<pre style="margin: 0;">+<span id="LC2288" 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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<pre style="margin: 0;">+<span id="LC2289" class="line" lang="cpp"></span>
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2282
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2290
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<pre style="margin: 0;"> <span id="LC2290" class="line" lang="cpp"> <span class="nl">default:</span></span>
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2283
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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;">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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2284
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2292
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<pre style="margin: 0;"> <span id="LC2292" 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="2292" style="width: 35px; color: rgba(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="2300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2292,6 +2300,8 @@ void args_init(int argc, char **argv)</td>
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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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">optind</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span></span>
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2293
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2301
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<pre style="margin: 0;"> <span id="LC2301" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized string on command line (%s)"</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="p">]);</span></span>
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2294
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2302
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<pre style="margin: 0;"> <span id="LC2302" class="line" lang="cpp"></span>
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2303
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<pre style="margin: 0;">+<span id="LC2303" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* Below is a list of all command names, in alphabetical order. */</span></span>
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2304
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<pre style="margin: 0;">+<span id="LC2304" class="line" lang="cpp"></span>
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2295
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2305
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<pre style="margin: 0;"> <span id="LC2305" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">command_options</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num old_line" data-linenumber="2296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2296
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2306
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<pre style="margin: 0;"> <span id="LC2306" class="line" lang="cpp"> <span class="p">{</span></span>
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2297
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2307
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<pre style="margin: 0;"> <span id="LC2307" class="line" lang="cpp"> <span class="n" style="color: #333;">option_allpairs_global</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">@@ -2342,7 +2352,12 @@ void args_init(int argc, char **argv)</td>
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2342
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<pre style="margin: 0;"> <span id="LC2352" class="line" lang="cpp"></span>
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2343
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2353
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<pre style="margin: 0;"> <span id="LC2353" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">commands_count</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;">command_options</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">);</span></span>
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2344
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2354
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<pre style="margin: 0;"> <span id="LC2354" class="line" lang="cpp"></span>
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2345
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<pre style="margin: 0;">-<span id="LC2345" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">valid_options</span><span class="p">[][</span><span class="mi" style="color: #099;">91</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span></span>
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2355
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<pre style="margin: 0;">+<span id="LC2355" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2356
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<pre style="margin: 0;">+<span id="LC2356" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Below is a list of all the options that are valid for each command.</span></span>
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2357
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<pre style="margin: 0;">+<span id="LC2357" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> The first line is the command and the lines below are the valid options.</span></span>
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2358
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<pre style="margin: 0;">+<span id="LC2358" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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2359
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<pre style="margin: 0;">+<span id="LC2359" class="line" lang="cpp"></span>
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2360
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<pre style="margin: 0;">+<span id="LC2360" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">valid_options</span><span class="p">[][</span><span class="mi" style="color: #099;">92</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span></span>
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2346
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2361
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<pre style="margin: 0;"> <span id="LC2361" class="line" lang="cpp"> <span class="p">{</span></span>
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2347
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2362
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<pre style="margin: 0;"> <span id="LC2362" class="line" lang="cpp"> <span class="p">{</span></span>
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2348
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2363
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<pre style="margin: 0;"> <span id="LC2363" class="line" lang="cpp"> <span class="n" style="color: #333;">option_allpairs_global</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2400" style="width: 35px; color: rgba(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="2415" style="width: 35px; color: rgba(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">@@ -2400,6 +2415,7 @@ void args_init(int argc, char **argv)</td>
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2400
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2415
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<pre style="margin: 0;"> <span id="LC2415" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
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2401
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2416
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<pre style="margin: 0;"> <span id="LC2416" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
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2402
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2417
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<pre style="margin: 0;"> <span id="LC2417" 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 old_line" data-linenumber="2403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2418
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<pre style="margin: 0;">+<span id="LC2418" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
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2403
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<td class="diff-line-num new_line" data-linenumber="2419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2419
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<pre style="margin: 0;"> <span id="LC2419" 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 old_line" data-linenumber="2404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2404
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<td class="diff-line-num new_line" data-linenumber="2420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2420
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<pre style="margin: 0;"> <span id="LC2420" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rightjust</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="2405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2405
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2421
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<pre style="margin: 0;"> <span id="LC2421" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rowlen</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2488" style="width: 35px; color: rgba(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="2504" style="width: 35px; color: rgba(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">@@ -2488,6 +2504,7 @@ void args_init(int argc, char **argv)</td>
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2488
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2504
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<pre style="margin: 0;"> <span id="LC2504" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
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2489
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<td class="diff-line-num new_line" data-linenumber="2505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2505
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<pre style="margin: 0;"> <span id="LC2505" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="2490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2490
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<td class="diff-line-num new_line" data-linenumber="2506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2506
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2506" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2491" style="width: 35px; color: rgba(0,0,0,0.3); 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="2507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2507
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<pre style="margin: 0;">+<span id="LC2507" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2491
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<td class="diff-line-num new_line" data-linenumber="2508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2508
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<pre style="margin: 0;"> <span id="LC2508" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2492
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<td class="diff-line-num new_line" data-linenumber="2509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2509
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2509" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rightjust</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2493
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<td class="diff-line-num new_line" data-linenumber="2510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2510
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2510" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rowlen</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2578" style="width: 35px; color: rgba(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="2595" style="width: 35px; color: rgba(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">@@ -2578,6 +2595,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="2578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2578
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<td class="diff-line-num new_line" data-linenumber="2595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2595
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2595" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></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="2579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2579
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<td class="diff-line-num new_line" data-linenumber="2596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2596
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2596" 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 old_line" data-linenumber="2580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2580
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<td class="diff-line-num new_line" data-linenumber="2597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2597
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2597" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2598
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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="LC2598" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2581
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<td class="diff-line-num new_line" data-linenumber="2599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2599
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2599" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2582
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<td class="diff-line-num new_line" data-linenumber="2600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2600
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2600" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rightjust</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2583
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<td class="diff-line-num new_line" data-linenumber="2601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2601
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2601" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rowlen</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2668" style="width: 35px; color: rgba(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="2686" style="width: 35px; color: rgba(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">@@ -2668,6 +2686,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="2668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2668
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<td class="diff-line-num new_line" data-linenumber="2686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2686
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2686" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></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="2669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2669
</td>
<td class="diff-line-num new_line" data-linenumber="2687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2687
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2687" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></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="2670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2670
</td>
<td class="diff-line-num new_line" data-linenumber="2688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2688
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2688" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2689
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2689" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2671
</td>
<td class="diff-line-num new_line" data-linenumber="2690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2690
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2690" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2672
</td>
<td class="diff-line-num new_line" data-linenumber="2691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2691
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2691" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rightjust</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2673
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<td class="diff-line-num new_line" data-linenumber="2692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2692
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2692" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rowlen</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2760" style="width: 35px; color: rgba(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="2779" style="width: 35px; color: rgba(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">@@ -2760,6 +2779,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="2760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2760
</td>
<td class="diff-line-num new_line" data-linenumber="2779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2779
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2779" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2761
</td>
<td class="diff-line-num new_line" data-linenumber="2780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2780
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2780" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2762
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<td class="diff-line-num new_line" data-linenumber="2781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2781
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2781" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2763" style="width: 35px; color: rgba(0,0,0,0.3); 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="2782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2782
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2782" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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</tr>
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<td class="diff-line-num old_line" data-linenumber="2763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2763
</td>
<td class="diff-line-num new_line" data-linenumber="2783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2783
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2783" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></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="2764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2764
</td>
<td class="diff-line-num new_line" data-linenumber="2784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2784
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2784" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rightjust</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2765
</td>
<td class="diff-line-num new_line" data-linenumber="2785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2785
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2785" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rowlen</span><span class="p">,</span></span>
</pre>
</td>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2802" style="width: 35px; color: rgba(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="2822" style="width: 35px; color: rgba(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">@@ -2802,7 +2822,10 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="2802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2802
</td>
<td class="diff-line-num new_line" data-linenumber="2822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2822
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2822" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2803
</td>
<td class="diff-line-num new_line" data-linenumber="2823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2823
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2823" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2804
</td>
<td class="diff-line-num new_line" data-linenumber="2824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2824
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2824" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2825
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2825" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2805
</td>
<td class="diff-line-num new_line" data-linenumber="2826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2826
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2826" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2827
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2827" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2828
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2828" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2806
</td>
<td class="diff-line-num new_line" data-linenumber="2829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2829
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2829" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xee</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2807
</td>
<td class="diff-line-num new_line" data-linenumber="2830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2830
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2830" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span><span class="p">,</span></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="2808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2808
</td>
<td class="diff-line-num new_line" data-linenumber="2831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2831
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2831" 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>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2823" style="width: 35px; color: rgba(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="2846" style="width: 35px; color: rgba(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">@@ -2823,6 +2846,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="2823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2823
</td>
<td class="diff-line-num new_line" data-linenumber="2846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2846
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2846" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2824
</td>
<td class="diff-line-num new_line" data-linenumber="2847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2847
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2847" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2825
</td>
<td class="diff-line-num new_line" data-linenumber="2848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2848
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2848" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2849
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2849" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2826
</td>
<td class="diff-line-num new_line" data-linenumber="2850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2850
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2850" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2827
</td>
<td class="diff-line-num new_line" data-linenumber="2851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2851
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2851" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2828
</td>
<td class="diff-line-num new_line" data-linenumber="2852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2852
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2852" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2850" style="width: 35px; color: rgba(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="2874" style="width: 35px; color: rgba(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">@@ -2850,6 +2874,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="2850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2850
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<td class="diff-line-num new_line" data-linenumber="2874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2874
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<pre style="margin: 0;"> <span id="LC2874" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2851
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<td class="diff-line-num new_line" data-linenumber="2875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2875
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<pre style="margin: 0;"> <span id="LC2875" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="2852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2852
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<td class="diff-line-num new_line" data-linenumber="2876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2876
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<pre style="margin: 0;"> <span id="LC2876" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2853" style="width: 35px; color: rgba(0,0,0,0.3); 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="2877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2877
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<pre style="margin: 0;">+<span id="LC2877" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2853
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<td class="diff-line-num new_line" data-linenumber="2878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2878
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2878" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2854
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<td class="diff-line-num new_line" data-linenumber="2879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2879
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2879" 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 old_line" data-linenumber="2855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2855
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<td class="diff-line-num new_line" data-linenumber="2880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2880
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2880" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2887" style="width: 35px; color: rgba(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="2912" style="width: 35px; color: rgba(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">@@ -2887,6 +2912,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="2887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2887
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<td class="diff-line-num new_line" data-linenumber="2912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2912
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<pre style="margin: 0;"> <span id="LC2912" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2888
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<td class="diff-line-num new_line" data-linenumber="2913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2913
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2913" 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 old_line" data-linenumber="2889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2889
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<td class="diff-line-num new_line" data-linenumber="2914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2914
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2914" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2890" style="width: 35px; color: rgba(0,0,0,0.3); 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="2915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2915
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<pre style="margin: 0;">+<span id="LC2915" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2890
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<td class="diff-line-num new_line" data-linenumber="2916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2916
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<pre style="margin: 0;"> <span id="LC2916" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2891
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<td class="diff-line-num new_line" data-linenumber="2917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2917
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2917" 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 old_line" data-linenumber="2892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2892
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<td class="diff-line-num new_line" data-linenumber="2918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2918
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2918" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2959" style="width: 35px; color: rgba(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="2985" style="width: 35px; color: rgba(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">@@ -2959,6 +2985,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="2959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2959
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<td class="diff-line-num new_line" data-linenumber="2985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2985
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2985" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2960
</td>
<td class="diff-line-num new_line" data-linenumber="2986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2986
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2986" 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 old_line" data-linenumber="2961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2961
</td>
<td class="diff-line-num new_line" data-linenumber="2987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2987
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2987" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2988
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2988" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2962
</td>
<td class="diff-line-num new_line" data-linenumber="2989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2989
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2989" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2963
</td>
<td class="diff-line-num new_line" data-linenumber="2990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2990
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2990" class="line" lang="cpp"> <span class="n" style="color: #333;">option_reverse</span><span class="p">,</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2964
</td>
<td class="diff-line-num new_line" data-linenumber="2991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2991
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2991" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2985" style="width: 35px; color: rgba(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="3012" style="width: 35px; color: rgba(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">@@ -2985,8 +3012,11 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="2985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2985
</td>
<td class="diff-line-num new_line" data-linenumber="3012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3012
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3012" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
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2986
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<td class="diff-line-num new_line" data-linenumber="3013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3013
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3013" 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 old_line" data-linenumber="2987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2987
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<td class="diff-line-num new_line" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3014
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3014" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2988" style="width: 35px; color: rgba(0,0,0,0.3); 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="3015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3015
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<pre style="margin: 0;">+<span id="LC3015" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2988
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<td class="diff-line-num new_line" data-linenumber="3016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3016
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3016" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2989
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<td class="diff-line-num new_line" data-linenumber="3017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3017
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3017" class="line" lang="cpp"> <span class="n" style="color: #333;">option_reverse</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2990" style="width: 35px; color: rgba(0,0,0,0.3); 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="3018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3018
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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="LC3018" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3019
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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="LC3019" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></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="2990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2990
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<td class="diff-line-num new_line" data-linenumber="3020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3020
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3020" 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 old_line" data-linenumber="2991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2991
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<td class="diff-line-num new_line" data-linenumber="3021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3021
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3021" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xee</span><span class="p">,</span></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="2992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2992
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<td class="diff-line-num new_line" data-linenumber="3022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3022
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3022" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3028" style="width: 35px; color: rgba(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="3058" style="width: 35px; color: rgba(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">@@ -3028,8 +3058,11 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3028
</td>
<td class="diff-line-num new_line" data-linenumber="3058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3058
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3058" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3029
</td>
<td class="diff-line-num new_line" data-linenumber="3059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3059
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3059" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></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="3030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3030
</td>
<td class="diff-line-num new_line" data-linenumber="3060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3060
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3060" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3061
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3061" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3031
</td>
<td class="diff-line-num new_line" data-linenumber="3062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3062
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3062" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3032
</td>
<td class="diff-line-num new_line" data-linenumber="3063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3063
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3063" class="line" lang="cpp"> <span class="n" style="color: #333;">option_reverse</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3064
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3064" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3065
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3065" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3033
</td>
<td class="diff-line-num new_line" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3066
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3066" class="line" lang="cpp"> <span class="n" style="color: #333;">option_threads</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3034
</td>
<td class="diff-line-num new_line" data-linenumber="3067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3067
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3067" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xee</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3035
</td>
<td class="diff-line-num new_line" data-linenumber="3068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3068
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3068" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3118" style="width: 35px; color: rgba(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">@@ -3085,6 +3118,7 @@ void args_init(int argc, char **argv)</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_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
</td>
<td class="diff-line-num new_line" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3118
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3118" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3086
</td>
<td class="diff-line-num new_line" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3119
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3119" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
</pre>
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3087
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<td class="diff-line-num new_line" data-linenumber="3120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3120
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<pre style="margin: 0;"> <span id="LC3120" 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 old_line" data-linenumber="3088" style="width: 35px; color: rgba(0,0,0,0.3); 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="3121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3121
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<pre style="margin: 0;">+<span id="LC3121" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
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3088
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<td class="diff-line-num new_line" data-linenumber="3122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3122
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<pre style="margin: 0;"> <span id="LC3122" 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 old_line" data-linenumber="3089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3089
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<td class="diff-line-num new_line" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3123
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<pre style="margin: 0;"> <span id="LC3123" class="line" lang="cpp"> <span class="n" style="color: #333;">option_reverse</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3090
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<td class="diff-line-num new_line" data-linenumber="3124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3124
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<pre style="margin: 0;"> <span id="LC3124" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3114" style="width: 35px; color: rgba(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="3148" style="width: 35px; color: rgba(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">@@ -3114,7 +3148,10 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3114
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<td class="diff-line-num new_line" data-linenumber="3148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3148
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<pre style="margin: 0;"> <span id="LC3148" 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 old_line" data-linenumber="3115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3115
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<td class="diff-line-num new_line" data-linenumber="3149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3149
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<pre style="margin: 0;"> <span id="LC3149" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3116
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<td class="diff-line-num new_line" data-linenumber="3150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3150
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<pre style="margin: 0;"> <span id="LC3150" 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 old_line" data-linenumber="3117" style="width: 35px; color: rgba(0,0,0,0.3); 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="3151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3151
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<pre style="margin: 0;">+<span id="LC3151" 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 old_line" data-linenumber="3117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3117
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<td class="diff-line-num new_line" data-linenumber="3152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3152
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<pre style="margin: 0;"> <span id="LC3152" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); 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="3153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3153
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<pre style="margin: 0;">+<span id="LC3153" 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 old_line" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); 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="3154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3154
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<pre style="margin: 0;">+<span id="LC3154" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
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3118
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<td class="diff-line-num new_line" data-linenumber="3155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3155
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<pre style="margin: 0;"> <span id="LC3155" 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 old_line" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3119
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<td class="diff-line-num new_line" data-linenumber="3156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3156
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<pre style="margin: 0;"> <span id="LC3156" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xee</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3120
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<td class="diff-line-num new_line" data-linenumber="3157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3157
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<pre style="margin: 0;"> <span id="LC3157" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3122" style="width: 35px; color: rgba(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="3159" style="width: 35px; color: rgba(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">@@ -3122,6 +3159,7 @@ void args_init(int argc, char **argv)</td>
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3122
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<td class="diff-line-num new_line" data-linenumber="3159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3159
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<pre style="margin: 0;"> <span id="LC3159" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3123
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<td class="diff-line-num new_line" data-linenumber="3160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3160
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<pre style="margin: 0;"> <span id="LC3160" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">option_fastx_getseqs</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3124
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<td class="diff-line-num new_line" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3161
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<pre style="margin: 0;"> <span id="LC3161" class="line" lang="cpp"> <span class="n" style="color: #333;">option_bzip2_decompress</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3125" style="width: 35px; color: rgba(0,0,0,0.3); 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="3162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3162
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<pre style="margin: 0;">+<span id="LC3162" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fasta_width</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3125
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<td class="diff-line-num new_line" data-linenumber="3163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3163
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3163" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastaout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3126
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<td class="diff-line-num new_line" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3164
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3164" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_ascii</span><span class="p">,</span></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="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">
3127
</td>
<td class="diff-line-num new_line" data-linenumber="3165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3165
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3165" class="line" lang="cpp"> <span class="n" style="color: #333;">option_fastq_qmax</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3143" style="width: 35px; color: rgba(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="3181" style="width: 35px; color: rgba(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">@@ -3143,7 +3181,10 @@ void args_init(int argc, char **argv)</td>
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3143
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<td class="diff-line-num new_line" data-linenumber="3181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3181
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<pre style="margin: 0;"> <span id="LC3181" 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 old_line" data-linenumber="3144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3144
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<td class="diff-line-num new_line" data-linenumber="3182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3182
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<pre style="margin: 0;"> <span id="LC3182" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3145
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<td class="diff-line-num new_line" data-linenumber="3183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3183
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<pre style="margin: 0;"> <span id="LC3183" 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 old_line" data-linenumber="3146" style="width: 35px; color: rgba(0,0,0,0.3); 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="3184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3184
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<pre style="margin: 0;">+<span id="LC3184" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
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3146
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<td class="diff-line-num new_line" data-linenumber="3185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3185
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<pre style="margin: 0;"> <span id="LC3185" 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 old_line" data-linenumber="3147" style="width: 35px; color: rgba(0,0,0,0.3); 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="3186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3186
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<pre style="margin: 0;">+<span id="LC3186" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3147" style="width: 35px; color: rgba(0,0,0,0.3); 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="3187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3187
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<pre style="margin: 0;">+<span id="LC3187" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3147
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<td class="diff-line-num new_line" data-linenumber="3188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3188
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<pre style="margin: 0;"> <span id="LC3188" class="line" lang="cpp"> <span class="n" style="color: #333;">option_threads</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3148
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<td class="diff-line-num new_line" data-linenumber="3189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3189
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<pre style="margin: 0;"> <span id="LC3189" 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 old_line" data-linenumber="3149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3149
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<td class="diff-line-num new_line" data-linenumber="3190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3190
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<pre style="margin: 0;"> <span id="LC3190" 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 unfold js-unfold old_line" data-linenumber="3169" style="width: 35px; color: rgba(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="3210" style="width: 35px; color: rgba(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">@@ -3169,7 +3210,10 @@ void args_init(int argc, char **argv)</td>
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3169
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<td class="diff-line-num new_line" data-linenumber="3210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3210
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<pre style="margin: 0;"> <span id="LC3210" 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 old_line" data-linenumber="3170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3170
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<td class="diff-line-num new_line" data-linenumber="3211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3211
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<pre style="margin: 0;"> <span id="LC3211" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3171
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<td class="diff-line-num new_line" data-linenumber="3212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3212
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<pre style="margin: 0;"> <span id="LC3212" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); 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="3213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3213
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<pre style="margin: 0;">+<span id="LC3213" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3172
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<td class="diff-line-num new_line" data-linenumber="3214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3214
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<pre style="margin: 0;"> <span id="LC3214" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); 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="3215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3215
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<pre style="margin: 0;">+<span id="LC3215" 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 old_line" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); 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="3216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3216
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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="LC3216" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3173
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<td class="diff-line-num new_line" data-linenumber="3217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3217
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<pre style="margin: 0;"> <span id="LC3217" class="line" lang="cpp"> <span class="n" style="color: #333;">option_subseq_end</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3174
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<td class="diff-line-num new_line" data-linenumber="3218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3218
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<pre style="margin: 0;"> <span id="LC3218" class="line" lang="cpp"> <span class="n" style="color: #333;">option_subseq_start</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3175
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<td class="diff-line-num new_line" data-linenumber="3219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3219
</td>
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<pre style="margin: 0;"> <span id="LC3219" 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 unfold js-unfold old_line" data-linenumber="3197" style="width: 35px; color: rgba(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="3241" style="width: 35px; color: rgba(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">@@ -3197,7 +3241,10 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3197
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<td class="diff-line-num new_line" data-linenumber="3241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3241
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3241" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></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="3198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3198
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<td class="diff-line-num new_line" data-linenumber="3242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3242
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3242" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
</pre>
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3199
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<td class="diff-line-num new_line" data-linenumber="3243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3243
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<pre style="margin: 0;"> <span id="LC3243" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3244
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<pre style="margin: 0;">+<span id="LC3244" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
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3200
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<td class="diff-line-num new_line" data-linenumber="3245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3245
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<pre style="margin: 0;"> <span id="LC3245" 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="3246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3246
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<pre style="margin: 0;">+<span id="LC3246" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3201" style="width: 35px; color: rgba(0,0,0,0.3); 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="3247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3247
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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="LC3247" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3201
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<td class="diff-line-num new_line" data-linenumber="3248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3248
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3248" 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 old_line" data-linenumber="3202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3202
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<td class="diff-line-num new_line" data-linenumber="3249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3249
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<pre style="margin: 0;"> <span id="LC3249" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xee</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3203
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<td class="diff-line-num new_line" data-linenumber="3250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3250
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<pre style="margin: 0;"> <span id="LC3250" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3220" style="width: 35px; color: rgba(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="3267" style="width: 35px; color: rgba(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">@@ -3220,7 +3267,10 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3220
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<td class="diff-line-num new_line" data-linenumber="3267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3267
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<pre style="margin: 0;"> <span id="LC3267" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3221
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<td class="diff-line-num new_line" data-linenumber="3268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3268
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<pre style="margin: 0;"> <span id="LC3268" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3222
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<td class="diff-line-num new_line" data-linenumber="3269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3269
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<pre style="margin: 0;"> <span id="LC3269" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3223" style="width: 35px; color: rgba(0,0,0,0.3); 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="3270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3270
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<pre style="margin: 0;">+<span id="LC3270" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3223
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<td class="diff-line-num new_line" data-linenumber="3271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3271
</td>
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<pre style="margin: 0;"> <span id="LC3271" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3224" style="width: 35px; color: rgba(0,0,0,0.3); 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="3272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3272
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<pre style="margin: 0;">+<span id="LC3272" 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 old_line" data-linenumber="3224" style="width: 35px; color: rgba(0,0,0,0.3); 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="3273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3273
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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="LC3273" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
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3224
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<td class="diff-line-num new_line" data-linenumber="3274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3274
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<pre style="margin: 0;"> <span id="LC3274" 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 old_line" data-linenumber="3225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3225
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<td class="diff-line-num new_line" data-linenumber="3275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3275
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3275" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xee</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3226
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<td class="diff-line-num new_line" data-linenumber="3276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3276
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3276" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3245" style="width: 35px; color: rgba(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="3295" style="width: 35px; color: rgba(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">@@ -3245,6 +3295,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3245
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<td class="diff-line-num new_line" data-linenumber="3295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3295
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3295" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></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="3246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3246
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<td class="diff-line-num new_line" data-linenumber="3296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3296
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3296" 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 old_line" data-linenumber="3247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3247
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<td class="diff-line-num new_line" data-linenumber="3297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3297
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3297" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3298
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3298" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3248
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<td class="diff-line-num new_line" data-linenumber="3299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3299
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3299" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3249
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<td class="diff-line-num new_line" data-linenumber="3300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3300
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<pre style="margin: 0;"> <span id="LC3300" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sample_pct</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3250
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<td class="diff-line-num new_line" data-linenumber="3301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3301
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<pre style="margin: 0;"> <span id="LC3301" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sample_size</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3299" style="width: 35px; color: rgba(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="3350" style="width: 35px; color: rgba(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">@@ -3299,7 +3350,10 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3299
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<td class="diff-line-num new_line" data-linenumber="3350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3350
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3350" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3300
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<td class="diff-line-num new_line" data-linenumber="3351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3351
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3351" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3301
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<td class="diff-line-num new_line" data-linenumber="3352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3352
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3352" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3302" style="width: 35px; color: rgba(0,0,0,0.3); 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="3353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3353
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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="LC3353" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3302
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<td class="diff-line-num new_line" data-linenumber="3354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3354
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3354" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3303" style="width: 35px; color: rgba(0,0,0,0.3); 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="3355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3355
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<pre style="margin: 0;">+<span id="LC3355" 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 old_line" data-linenumber="3303" style="width: 35px; color: rgba(0,0,0,0.3); 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="3356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3356
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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="LC3356" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3303
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<td class="diff-line-num new_line" data-linenumber="3357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3357
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<pre style="margin: 0;"> <span id="LC3357" 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 old_line" data-linenumber="3304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3304
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<td class="diff-line-num new_line" data-linenumber="3358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3358
</td>
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<pre style="margin: 0;"> <span id="LC3358" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xee</span><span class="p">,</span></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="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3305
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<td class="diff-line-num new_line" data-linenumber="3359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3359
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3359" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3317" style="width: 35px; color: rgba(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="3371" style="width: 35px; color: rgba(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">@@ -3317,6 +3371,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3317
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<td class="diff-line-num new_line" data-linenumber="3371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3371
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3371" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3318
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<td class="diff-line-num new_line" data-linenumber="3372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3372
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3372" 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 old_line" data-linenumber="3319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3319
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<td class="diff-line-num new_line" data-linenumber="3373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3373
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3373" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3320" style="width: 35px; color: rgba(0,0,0,0.3); 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="3374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3374
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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="LC3374" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3320
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<td class="diff-line-num new_line" data-linenumber="3375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3375
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3375" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3321
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<td class="diff-line-num new_line" data-linenumber="3376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3376
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3376" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></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="3322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3322
</td>
<td class="diff-line-num new_line" data-linenumber="3377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3377
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3377" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3365" style="width: 35px; color: rgba(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="3420" style="width: 35px; color: rgba(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">@@ -3365,6 +3420,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3365
</td>
<td class="diff-line-num new_line" data-linenumber="3420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3420
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3420" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3366
</td>
<td class="diff-line-num new_line" data-linenumber="3421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3421
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3421" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3367
</td>
<td class="diff-line-num 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">
3422
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3422" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3368" style="width: 35px; color: rgba(0,0,0,0.3); 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="3423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3423
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<pre style="margin: 0;">+<span id="LC3423" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3368
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<td class="diff-line-num new_line" data-linenumber="3424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3424
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<pre style="margin: 0;"> <span id="LC3424" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3369
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<td class="diff-line-num new_line" data-linenumber="3425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3425
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<pre style="margin: 0;"> <span id="LC3425" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rowlen</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3370
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<td class="diff-line-num new_line" data-linenumber="3426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3426
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3426" class="line" lang="cpp"> <span class="n" style="color: #333;">option_samheader</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3391" style="width: 35px; color: rgba(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="3447" style="width: 35px; color: rgba(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">@@ -3391,7 +3447,13 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3391
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<td class="diff-line-num new_line" data-linenumber="3447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3447
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<pre style="margin: 0;"> <span id="LC3447" class="line" lang="cpp"> <span class="n" style="color: #333;">option_log</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3392
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<td class="diff-line-num new_line" data-linenumber="3448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3448
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3448" class="line" lang="cpp"> <span class="n" style="color: #333;">option_no_progress</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3393
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<td class="diff-line-num new_line" data-linenumber="3449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3449
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<pre style="margin: 0;"> <span id="LC3449" class="line" lang="cpp"> <span class="n" style="color: #333;">option_quiet</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3394" style="width: 35px; color: rgba(0,0,0,0.3); 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="3450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3450
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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="LC3450" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3394" style="width: 35px; color: rgba(0,0,0,0.3); 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="3451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3451
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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="LC3451" 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 old_line" data-linenumber="3394" style="width: 35px; color: rgba(0,0,0,0.3); 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="3452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3452
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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="LC3452" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3394" style="width: 35px; color: rgba(0,0,0,0.3); 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="3453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3453
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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="LC3453" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3394" style="width: 35px; color: rgba(0,0,0,0.3); 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="3454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3454
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<pre style="margin: 0;">+<span id="LC3454" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3394
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<td class="diff-line-num new_line" data-linenumber="3455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3455
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3455" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sff_clip</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3395" style="width: 35px; color: rgba(0,0,0,0.3); 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="3456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3456
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3456" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></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="3395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3395
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<td class="diff-line-num new_line" data-linenumber="3457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3457
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3457" class="line" lang="cpp"> <span class="n" style="color: #333;">option_threads</span><span class="p">,</span></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="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
</td>
<td class="diff-line-num new_line" data-linenumber="3458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3458
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3458" 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>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<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
</td>
<td class="diff-line-num new_line" data-linenumber="3459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3459
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3459" class="line" lang="cpp"></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3413" style="width: 35px; color: rgba(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="3475" style="width: 35px; color: rgba(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">@@ -3413,7 +3475,9 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3413
</td>
<td class="diff-line-num new_line" data-linenumber="3475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3475
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3475" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3414
</td>
<td class="diff-line-num new_line" data-linenumber="3476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3476
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3476" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3415
</td>
<td class="diff-line-num new_line" data-linenumber="3477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3477
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3477" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3478
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3478" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3416
</td>
<td class="diff-line-num new_line" data-linenumber="3479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3479
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3479" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3417" style="width: 35px; color: rgba(0,0,0,0.3); 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="3480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3480
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<pre style="margin: 0;">+<span id="LC3480" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3417
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<td class="diff-line-num new_line" data-linenumber="3481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3481
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<pre style="margin: 0;"> <span id="LC3481" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3418
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<td class="diff-line-num new_line" data-linenumber="3482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3482
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<pre style="margin: 0;"> <span id="LC3482" class="line" lang="cpp"> <span class="n" style="color: #333;">option_threads</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3419
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<td class="diff-line-num new_line" data-linenumber="3483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3483
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<pre style="margin: 0;"> <span id="LC3483" class="line" lang="cpp"> <span class="n" style="color: #333;">option_topn</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3457" style="width: 35px; color: rgba(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="3521" style="width: 35px; color: rgba(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">@@ -3457,7 +3521,9 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3457
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<td class="diff-line-num new_line" data-linenumber="3521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3521
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<pre style="margin: 0;"> <span id="LC3521" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3458
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<td class="diff-line-num new_line" data-linenumber="3522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3522
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<pre style="margin: 0;"> <span id="LC3522" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="3459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3459
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<td class="diff-line-num new_line" data-linenumber="3523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3523
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3523" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3460" style="width: 35px; color: rgba(0,0,0,0.3); 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="3524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3524
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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="LC3524" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3460
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<td class="diff-line-num new_line" data-linenumber="3525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3525
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3525" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3461" style="width: 35px; color: rgba(0,0,0,0.3); 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="3526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3526
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<pre style="margin: 0;">+<span id="LC3526" 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 old_line" data-linenumber="3461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3461
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<td class="diff-line-num new_line" data-linenumber="3527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3527
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<pre style="margin: 0;"> <span id="LC3527" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3462
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<td class="diff-line-num new_line" data-linenumber="3528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3528
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<pre style="margin: 0;"> <span id="LC3528" 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 old_line" data-linenumber="3463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3463
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<td class="diff-line-num new_line" data-linenumber="3529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3529
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3529" class="line" lang="cpp"> <span class="n" style="color: #333;">option_topn</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3484" style="width: 35px; color: rgba(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="3550" style="width: 35px; color: rgba(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">@@ -3484,7 +3550,9 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3484
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<td class="diff-line-num new_line" data-linenumber="3550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3550
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3550" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3485
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<td class="diff-line-num new_line" data-linenumber="3551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3551
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3551" 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 old_line" data-linenumber="3486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3486
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<td class="diff-line-num new_line" data-linenumber="3552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3552
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3552" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3487" style="width: 35px; color: rgba(0,0,0,0.3); 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="3553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3553
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<pre style="margin: 0;">+<span id="LC3553" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3487
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<td class="diff-line-num new_line" data-linenumber="3554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3554
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<pre style="margin: 0;"> <span id="LC3554" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3488" style="width: 35px; color: rgba(0,0,0,0.3); 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="3555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3555
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<pre style="margin: 0;">+<span id="LC3555" 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 old_line" data-linenumber="3488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3488
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<td class="diff-line-num new_line" data-linenumber="3556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3556
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3556" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3489
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<td class="diff-line-num new_line" data-linenumber="3557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3557
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3557" 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 old_line" data-linenumber="3490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3490
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<td class="diff-line-num new_line" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3558
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3558" class="line" lang="cpp"> <span class="n" style="color: #333;">option_topn</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3517" style="width: 35px; color: rgba(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="3585" style="width: 35px; color: rgba(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">@@ -3517,6 +3585,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3517
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<td class="diff-line-num new_line" data-linenumber="3585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3585
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3585" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3518
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<td class="diff-line-num new_line" data-linenumber="3586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3586
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3586" 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 old_line" data-linenumber="3519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3519
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<td class="diff-line-num new_line" data-linenumber="3587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3587
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3587" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3520" style="width: 35px; color: rgba(0,0,0,0.3); 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="3588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3588
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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="LC3588" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3520
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<td class="diff-line-num new_line" data-linenumber="3589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3589
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3589" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3521
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<td class="diff-line-num new_line" data-linenumber="3590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3590
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3590" 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 old_line" data-linenumber="3522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3522
</td>
<td class="diff-line-num new_line" data-linenumber="3591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3591
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3591" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3554" style="width: 35px; color: rgba(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="3623" style="width: 35px; color: rgba(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">@@ -3554,6 +3623,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3554
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<td class="diff-line-num new_line" data-linenumber="3623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3623
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3623" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></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="3555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3555
</td>
<td class="diff-line-num new_line" data-linenumber="3624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3624
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3624" 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 old_line" data-linenumber="3556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3556
</td>
<td class="diff-line-num new_line" data-linenumber="3625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3625
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3625" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3626
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3626" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3557
</td>
<td class="diff-line-num new_line" data-linenumber="3627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3627
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3627" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3558
</td>
<td class="diff-line-num new_line" data-linenumber="3628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3628
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3628" 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 old_line" data-linenumber="3559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3559
</td>
<td class="diff-line-num new_line" data-linenumber="3629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3629
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3629" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3591" style="width: 35px; color: rgba(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="3661" style="width: 35px; color: rgba(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">@@ -3591,6 +3661,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3591
</td>
<td class="diff-line-num new_line" data-linenumber="3661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3661
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3661" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3592
</td>
<td class="diff-line-num new_line" data-linenumber="3662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3662
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3662" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></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="3593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3593
</td>
<td class="diff-line-num new_line" data-linenumber="3663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3663
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3663" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3664
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3664" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3594
</td>
<td class="diff-line-num new_line" data-linenumber="3665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3665
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3665" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
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</tr>
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<td class="diff-line-num old_line" data-linenumber="3595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3595
</td>
<td class="diff-line-num new_line" data-linenumber="3666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3666
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3666" 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 old_line" data-linenumber="3596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3596
</td>
<td class="diff-line-num new_line" data-linenumber="3667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3667
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3667" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3630" style="width: 35px; color: rgba(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="3701" style="width: 35px; color: rgba(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">@@ -3630,6 +3701,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3630
</td>
<td class="diff-line-num new_line" data-linenumber="3701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3701
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3701" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
</td>
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<td class="diff-line-num old_line" data-linenumber="3631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3631
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<td class="diff-line-num new_line" data-linenumber="3702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3702
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3702" 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 old_line" data-linenumber="3632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3632
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<td class="diff-line-num new_line" data-linenumber="3703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3703
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3703" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3633" style="width: 35px; color: rgba(0,0,0,0.3); 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="3704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3704
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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="LC3704" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3633
</td>
<td class="diff-line-num new_line" data-linenumber="3705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3705
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3705" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></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="3634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3634
</td>
<td class="diff-line-num new_line" data-linenumber="3706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3706
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3706" class="line" lang="cpp"> <span class="n" style="color: #333;">option_self</span><span class="p">,</span></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="3635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3635
</td>
<td class="diff-line-num new_line" data-linenumber="3707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3707
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3707" class="line" lang="cpp"> <span class="n" style="color: #333;">option_selfid</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3654" style="width: 35px; color: rgba(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="3726" style="width: 35px; color: rgba(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">@@ -3654,7 +3726,10 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3654
</td>
<td class="diff-line-num new_line" data-linenumber="3726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3726
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3726" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></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="3655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3655
</td>
<td class="diff-line-num new_line" data-linenumber="3727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3727
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3727" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></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="3656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3656
</td>
<td class="diff-line-num new_line" data-linenumber="3728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3728
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3728" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3729
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3729" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3657
</td>
<td class="diff-line-num new_line" data-linenumber="3730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3730
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3730" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3731
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3731" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizein</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3732
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3732" class="line" lang="cpp"> <span class="n" style="color: #333;">option_sizeout</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3658
</td>
<td class="diff-line-num new_line" data-linenumber="3733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3733
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3733" class="line" lang="cpp"> <span class="n" style="color: #333;">option_threads</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3659
</td>
<td class="diff-line-num new_line" data-linenumber="3734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3734
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3734" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xee</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3660
</td>
<td class="diff-line-num new_line" data-linenumber="3735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3735
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3735" class="line" lang="cpp"> <span class="n" style="color: #333;">option_xsize</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3734" style="width: 35px; color: rgba(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="3809" style="width: 35px; color: rgba(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">@@ -3734,6 +3809,7 @@ void args_init(int argc, char **argv)</td>
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<td class="diff-line-num old_line" data-linenumber="3734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3734
</td>
<td class="diff-line-num new_line" data-linenumber="3809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3809
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3809" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3735
</td>
<td class="diff-line-num new_line" data-linenumber="3810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3810
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3810" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_keep</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3736
</td>
<td class="diff-line-num new_line" data-linenumber="3811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3811
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3811" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_md5</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="3737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3812
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3812" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_self</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3737
</td>
<td class="diff-line-num new_line" data-linenumber="3813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3813
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3813" class="line" lang="cpp"> <span class="n" style="color: #333;">option_relabel_sha1</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3738
</td>
<td class="diff-line-num new_line" data-linenumber="3814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3814
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3814" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rightjust</span><span class="p">,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3739
</td>
<td class="diff-line-num new_line" data-linenumber="3815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3815
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3815" class="line" lang="cpp"> <span class="n" style="color: #333;">option_rowlen</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4000" style="width: 35px; color: rgba(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">@@ -3924,14 +4000,9 @@ void args_init(int argc, char **argv)</td>
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3924
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<td class="diff-line-num new_line" data-linenumber="4000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4000
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<pre style="margin: 0;"> <span id="LC4000" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_sample_size</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="3925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3925
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<td class="diff-line-num new_line" data-linenumber="4001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4001
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<pre style="margin: 0;"> <span id="LC4001" 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 --sample_size must not be negative"</span><span class="p">);</span></span>
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3926
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4002
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<pre style="margin: 0;"> <span id="LC4002" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="3927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3927
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<td class="diff-line-num new_line old" data-linenumber="4003" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3927" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_relabel_sha1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">opt_relabel_md5</span><span class="p">)</span></span>
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3928
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<td class="diff-line-num new_line old" data-linenumber="4003" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3928" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Specify either --relabel_sha1 or --relabel_md5, not both"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3929
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<td class="diff-line-num new_line old" data-linenumber="4003" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3929" class="line" lang="cpp"></span>
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3930
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<td class="diff-line-num new_line old" data-linenumber="4003" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3930" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_relabel</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">opt_relabel_md5</span><span class="p">)</span></span>
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3931
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<td class="diff-line-num new_line old" data-linenumber="4003" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3931" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Specify either --relabel or --relabel_md5, not both"</span><span class="p">);</span></span>
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3932
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<td class="diff-line-num new_line old" data-linenumber="4003" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3932" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="3933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3933
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<td class="diff-line-num new_line old" data-linenumber="4003" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3933" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_relabel</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">opt_relabel_sha1</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3934
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<pre style="margin: 0;">-<span id="LC3934" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Specify either --relabel or --relabel_sha1, not both"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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4003
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<pre style="margin: 0;">+<span id="LC4003" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(((</span><span class="n" style="color: #333;">opt_relabel</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="o" style="font-weight: 600;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4004
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<pre style="margin: 0;">+<span id="LC4004" class="line" lang="cpp"> <span class="n" style="color: #333;">opt_relabel_md5</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opt_relabel_self</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opt_relabel_sha1</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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<td class="diff-line-num new new_line" data-linenumber="4005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4005
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<pre style="margin: 0;">+<span id="LC4005" class="line" lang="cpp"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Specify only one of --relabel, --relabel_self, --relabel_sha1, or --relabel_md5"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="3935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3935
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<td class="diff-line-num new_line" data-linenumber="4006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4006
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<pre style="margin: 0;"> <span id="LC4006" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="3936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3936
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<td class="diff-line-num new_line" data-linenumber="4007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4007
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<pre style="margin: 0;"> <span id="LC4007" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_fastq_tail</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="3937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3937
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<td class="diff-line-num new_line" data-linenumber="4008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4008
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<pre style="margin: 0;"> <span id="LC4008" 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 --fastq_tail must be positive"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4139" style="width: 35px; color: rgba(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="4210" style="width: 35px; color: rgba(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">@@ -4139,6 +4210,7 @@ void cmd_help()</td>
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4139
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<td class="diff-line-num new_line" data-linenumber="4210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4210
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<pre style="margin: 0;"> <span id="LC4210" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel STRING relabel nonchimeras with this prefix string</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="4140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4140
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<td class="diff-line-num new_line" data-linenumber="4211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4211
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<pre style="margin: 0;"> <span id="LC4211" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_keep keep the old label after the new when relabelling</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="4141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4141
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<td class="diff-line-num new_line" data-linenumber="4212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4212
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<pre style="margin: 0;"> <span id="LC4212" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_md5 relabel with md5 digest of normalized sequence</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4142" style="width: 35px; color: rgba(0,0,0,0.3); 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="4213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4213
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<pre style="margin: 0;">+<span id="LC4213" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_self relabel with the sequence itself as label</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4142
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<td class="diff-line-num new_line" data-linenumber="4214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4214
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<pre style="margin: 0;"> <span id="LC4214" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_sha1 relabel with sha1 digest of normalized sequence</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4143
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<td class="diff-line-num new_line" data-linenumber="4215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4215
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<pre style="margin: 0;"> <span id="LC4215" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --sizeout include abundance information when relabelling</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4144
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<td class="diff-line-num new_line" data-linenumber="4216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4216
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<pre style="margin: 0;"> <span id="LC4216" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --uchimealns FILENAME output chimera alignments to file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4175" style="width: 35px; color: rgba(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="4247" style="width: 35px; color: rgba(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">@@ -4175,6 +4247,7 @@ void cmd_help()</td>
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<td class="diff-line-num old_line" data-linenumber="4175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4175
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<td class="diff-line-num new_line" data-linenumber="4247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4247
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<pre style="margin: 0;"> <span id="LC4247" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel STRING relabel centroids with this prefix string</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4176
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<td class="diff-line-num new_line" data-linenumber="4248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4248
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<pre style="margin: 0;"> <span id="LC4248" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_keep keep the old label after the new when relabelling</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4177
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<td class="diff-line-num new_line" data-linenumber="4249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4249
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<pre style="margin: 0;"> <span id="LC4249" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_md5 relabel with md5 digest of normalized sequence</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4178" style="width: 35px; color: rgba(0,0,0,0.3); 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="4250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4250
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<pre style="margin: 0;">+<span id="LC4250" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_self relabel with the sequence itself as label</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4178
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<td class="diff-line-num new_line" data-linenumber="4251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4251
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<pre style="margin: 0;"> <span id="LC4251" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_sha1 relabel with sha1 digest of normalized sequence</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4179
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<td class="diff-line-num new_line" data-linenumber="4252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4252
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<pre style="margin: 0;"> <span id="LC4252" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --sizeorder sort accepted centroids by abundance, AGC</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4180
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<td class="diff-line-num new_line" data-linenumber="4253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4253
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<pre style="margin: 0;"> <span id="LC4253" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --sizeout write cluster abundances to centroid file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4205" style="width: 35px; color: rgba(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="4278" style="width: 35px; color: rgba(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">@@ -4205,6 +4278,7 @@ void cmd_help()</td>
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4205
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<td class="diff-line-num new_line" data-linenumber="4278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4278
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<pre style="margin: 0;"> <span id="LC4278" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel STRING relabel with this prefix string</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4206
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<td class="diff-line-num new_line" data-linenumber="4279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4279
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4279" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_keep keep the old label after the new when relabelling</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4207
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<td class="diff-line-num new_line" data-linenumber="4280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4280
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<pre style="margin: 0;"> <span id="LC4280" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_md5 relabel with md5 digest of normalized sequence</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4208" style="width: 35px; color: rgba(0,0,0,0.3); 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="cpp"> <span class="s" style="color: #d14;">" --relabel_self relabel with the sequence itself as label</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4208
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<td class="diff-line-num new_line" data-linenumber="4282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4282
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<pre style="margin: 0;"> <span id="LC4282" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_sha1 relabel with sha1 digest of normalized sequence</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4209
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<td class="diff-line-num new_line" data-linenumber="4283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4283
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<pre style="margin: 0;"> <span id="LC4283" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --sizeout write abundance annotation to output</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4210
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<td class="diff-line-num new_line" data-linenumber="4284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4284
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<pre style="margin: 0;"> <span id="LC4284" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --topn INT output only n most abundant sequences after derep</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4418" style="width: 35px; color: rgba(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="4492" style="width: 35px; color: rgba(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">@@ -4418,6 +4492,7 @@ void cmd_help()</td>
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4418
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<td class="diff-line-num new_line" data-linenumber="4492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4492
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<pre style="margin: 0;"> <span id="LC4492" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel STRING relabel sequences with this prefix string</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4419
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<td class="diff-line-num new_line" data-linenumber="4493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4493
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<pre style="margin: 0;"> <span id="LC4493" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_keep keep the old label after the new when relabelling</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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4420
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4494
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<pre style="margin: 0;"> <span id="LC4494" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_md5 relabel with md5 digest of normalized sequence</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4495
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<pre style="margin: 0;">+<span id="LC4495" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_self relabel with the sequence itself as label</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4421
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4496
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<pre style="margin: 0;"> <span id="LC4496" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_sha1 relabel with sha1 digest of normalized sequence</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4422
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4497
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<pre style="margin: 0;"> <span id="LC4497" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --sizeout include abundance information when relabelling</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="4423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4423
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<td class="diff-line-num new_line" data-linenumber="4498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4498
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<pre style="margin: 0;"> <span id="LC4498" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --topn INT output just first n sequences</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="4441" style="width: 35px; color: rgba(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="4516" style="width: 35px; color: rgba(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">@@ -4441,6 +4516,7 @@ void cmd_help()</td>
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4441
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<td class="diff-line-num new_line" data-linenumber="4516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4516
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<pre style="margin: 0;"> <span id="LC4516" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel STRING relabel sequences with this prefix string</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4442
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4517
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<pre style="margin: 0;"> <span id="LC4517" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_keep keep the old label after the new when relabelling</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4443
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4518
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<pre style="margin: 0;"> <span id="LC4518" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_md5 relabel with md5 digest of normalized sequence</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4519
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<pre style="margin: 0;">+<span id="LC4519" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_self relabel with the sequence itself as label</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4444
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4520
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<pre style="margin: 0;"> <span id="LC4520" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_sha1 relabel with sha1 digest of normalized sequence</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4445
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4521
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<pre style="margin: 0;"> <span id="LC4521" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --sizeout update abundance information in output</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4446
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4522
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<pre style="margin: 0;"> <span id="LC4522" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --xsize strip abundance information in output</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="4487" style="width: 35px; color: rgba(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="4563" style="width: 35px; color: rgba(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">@@ -4487,6 +4563,7 @@ void cmd_help()</td>
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4487
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4563
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<pre style="margin: 0;"> <span id="LC4563" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel STRING relabel filtered sequences with given prefix</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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4488
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4564
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<pre style="margin: 0;"> <span id="LC4564" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_keep keep the old label after the new when relabelling</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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4489
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4565
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<pre style="margin: 0;"> <span id="LC4565" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_md5 relabel filtered sequences with md5 digest</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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4566
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<pre style="margin: 0;">+<span id="LC4566" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_self relabel with the sequence itself as label</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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4490
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<td class="diff-line-num new_line" data-linenumber="4567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4567
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<pre style="margin: 0;"> <span id="LC4567" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --relabel_sha1 relabel filtered sequences with sha1 digest</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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4491
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4568
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<pre style="margin: 0;"> <span id="LC4568" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --sizeout include abundance information when relabelling</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4492
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4569
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<pre style="margin: 0;"> <span id="LC4569" 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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<li id="d5c50f833cab4828d6d2b3f54dda35a42237db09">
<a href="https://salsa.debian.org/med-team/vsearch/commit/a6e84605ff4ae3d2eb2fe51571bda5469e368a1e#d5c50f833cab4828d6d2b3f54dda35a42237db09"><strong>src/vsearch.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="265" style="width: 35px; color: rgba(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">@@ -265,6 +265,7 @@ extern bool opt_no_progress;</td>
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265
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">opt_quiet</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
266
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<td class="diff-line-num new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">opt_relabel_keep</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
267
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<td class="diff-line-num new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">opt_relabel_md5</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">opt_relabel_self</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
268
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<td class="diff-line-num new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">opt_relabel_sha1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
269
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<td class="diff-line-num new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">opt_samheader</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
270
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<td class="diff-line-num new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">opt_sff_clip</span><span class="p">;</span></span>
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