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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/8f9cb2d86c9d55fa125f18d7065bc4390550d5a2">8f9cb2d8</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-08-03T12:55:54Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.13.6</pre>
</li>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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<li class="file-stats">
<a href="#b7ca4efea9812be2ea989e558de10e419bd9cf39">
man/vsearch.1
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<li class="file-stats">
<a href="#b0109d980457466d1deec0f79c45e2b54114fdd5">
src/vsearch.cc
</a>
</li>
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/vsearch/commit/8f9cb2d86c9d55fa125f18d7065bc4390550d5a2#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<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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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>
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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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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"></span>
</pre>
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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/v2.13.<span class="idiff left right">5</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="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/v2.13.<span class="idiff left right">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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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"></span>
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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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<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/v2.13.<span class="idiff left right">5</span>.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown">tar xzf v2.13.<span class="idiff left right">5</span>.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown">cd vsearch-2.13.<span class="idiff left right">5</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">wget https://github.com/torognes/vsearch/archive/v2.13.<span class="idiff left right">6</span>.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown">tar xzf v2.13.<span class="idiff left right">6</span>.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown">cd vsearch-2.13.<span class="idiff left right">6</span></span>
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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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -78,43 +78,43 @@ Binary distributions are provided for x86-64 systems running GNU/Linux, macOS (v</td>
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78
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown">Download the appropriate executable for your system using the following commands if you are using a Linux x86_64 system:</span>
</pre>
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79
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown"></span>
</pre>
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80
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
</pre>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.13.<span class="idiff left right">5/vsearch-2.13.5</span>-linux-x86_64.tar.gz</span>
</pre>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.13.<span class="idiff left right">5</span>-linux-x86_64.tar.gz</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.13.<span class="idiff left right">6/vsearch-2.13.6</span>-linux-x86_64.tar.gz</span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.13.<span class="idiff left right">6</span>-linux-x86_64.tar.gz</span>
</pre>
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83
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"><span class="p">```</span></span>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"></span>
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85
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown">Or these commands if you are using a Linux ppc64le system:</span>
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86
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"></span>
</pre>
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87
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
</pre>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.13.<span class="idiff left right">5/vsearch-2.13.5</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-2.13.<span class="idiff left right">5</span>-linux-ppc64le.tar.gz</span>
</pre>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.13.<span class="idiff left right">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-2.13.<span class="idiff left right">6</span>-linux-ppc64le.tar.gz</span>
</pre>
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90
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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91
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91
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"></span>
</pre>
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92
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown">Or these commands if you are using a Linux aarch64 system:</span>
</pre>
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93
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"></span>
</pre>
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<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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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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/v2.13.<span class="idiff left right">5/vsearch-2.13.5</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>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.13.<span class="idiff left right">5</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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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/v2.13.<span class="idiff left right">6/vsearch-2.13.6</span>-linux-aarch64.tar.gz</span>
</pre>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.13.<span class="idiff left right">6</span>-linux-aarch64.tar.gz</span>
</pre>
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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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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"></span>
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99
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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>
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100
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
101
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
</pre>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.13.<span class="idiff left right">5/vsearch-2.13.5</span>-macos-x86_64.tar.gz</span>
</pre>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.13.<span class="idiff left right">5</span>-macos-x86_64.tar.gz</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown">wget https://github.com/torognes/vsearch/releases/download/v2.13.<span class="idiff left right">6/vsearch-2.13.6</span>-macos-x86_64.tar.gz</span>
</pre>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xzf vsearch-2.13.<span class="idiff left right">6</span>-macos-x86_64.tar.gz</span>
</pre>
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104
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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105
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105
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<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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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="markdown">Or if you are using Windows, download and extract (unzip) the contents of this file:</span>
</pre>
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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>
</pre>
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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
108
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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="markdown">https://github.com/torognes/vsearch/releases/download/v2.13.<span class="idiff left right">5/vsearch-2.13.5</span>-win-x86_64.zip</span>
</pre>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown">https://github.com/torognes/vsearch/releases/download/v2.13.<span class="idiff left right">6/vsearch-2.13.6</span>-win-x86_64.zip</span>
</pre>
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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>
</pre>
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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
111
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
112
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<td class="diff-line-num new_line old" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<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-2.13.<span class="idiff left">5-linux-x86_64`</span></span><span class="idiff"> or </span><span class="sb" style="color: #d14;"><span class="idiff right">`vsearch-2.13.5</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>
</pre>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown">Linux and Mac: You will now have the binary distribution in a folder called <span class="sb" style="color: #d14;">`vsearch-2.13.<span class="idiff left">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>
</pre>
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113
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
114
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<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-2.13.<span class="idiff left right">5</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="LC114" class="line" lang="markdown">Windows: You will now have the binary distribution in a folder called <span class="sb" style="color: #d14;">`vsearch-2.13.<span class="idiff left right">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="LC115" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Documentation**</span> The VSEARCH user's manual is available in the <span class="sb" style="color: #d14;">`man`</span> folder in the form of a <span class="p">[</span><span class="nv" style="color: #008080;">man page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/blob/master/man/vsearch.1</span><span class="p">)</span>. A pdf version (<span class="p">[</span><span class="nv" style="color: #008080;">vsearch_manual.pdf</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases/download/v2.13.<span class="idiff left">5/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/v2.13.5</span>/vsearch_manual.pdf</span><span class="p">)</span>) is also attached to the latest <span class="p">[</span><span class="nv" style="color: #008080;">release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Documentation**</span> The VSEARCH user's manual is available in the <span class="sb" style="color: #d14;">`man`</span> folder in the form of a <span class="p">[</span><span class="nv" style="color: #008080;">man page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/blob/master/man/vsearch.1</span><span class="p">)</span>. A pdf version (<span class="p">[</span><span class="nv" style="color: #008080;">vsearch_manual.pdf</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/torognes/vsearch/releases/download/v2.13.<span class="idiff left">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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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Packages, plugins, and wrappers</span></span>
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<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/vsearch/commit/8f9cb2d86c9d55fa125f18d7065bc4390550d5a2#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"># Process this file with autoconf to produce a configure script.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AC_PREREQ([2.63])</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">AC_INIT([vsearch], [2.13.<span class="idiff left right">5</span>], [torognes@ifi.uio.no])</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">AC_INIT([vsearch], [2.13.<span class="idiff left right">6</span>], [torognes@ifi.uio.no])</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">AC_CANONICAL_TARGET</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">AM_INIT_AUTOMAKE([subdir-objects])</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">AC_LANG([C++])</span>
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<a href="https://salsa.debian.org/med-team/vsearch/commit/8f9cb2d86c9d55fa125f18d7065bc4390550d5a2#b7ca4efea9812be2ea989e558de10e419bd9cf39"><strong>man/vsearch.1</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" ============================================================================</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH vsearch 1 "July 2, 2019" "version 2.13.<span class="idiff left right">4</span>" "USER COMMANDS"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH vsearch 1 "July 2, 2019" "version 2.13.<span class="idiff left right">6</span>" "USER COMMANDS"</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">.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="3841" style="width: 35px; color: rgba(0,0,0,0.3); 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="3841" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3841,6 +3841,9 @@ compilation on FreeBSD and NetBSD systems.</td>
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3841
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<td class="diff-line-num new_line" data-linenumber="3841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3841
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<pre style="margin: 0;"> <span id="LC3841" class="line" lang="plaintext">.BR v2.13.5\~ "released July 2nd, 2019"</span>
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<td class="diff-line-num old_line" data-linenumber="3842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3842
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3842
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<pre style="margin: 0;"> <span id="LC3842" class="line" lang="plaintext">Added cut command to fragment sequences at restriction sites. Silenced</span>
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3843
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3843
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<pre style="margin: 0;"> <span id="LC3843" class="line" lang="plaintext">output from the fastq_stats command if quiet option was given. Updated manual.</span>
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3844
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<pre style="margin: 0;">+<span id="LC3844" class="line" lang="plaintext">.TP</span>
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3845
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<pre style="margin: 0;">+<span id="LC3845" class="line" lang="plaintext">.BR v2.13.6\~ "released July 2nd, 2019"</span>
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3846
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<pre style="margin: 0;">+<span id="LC3846" class="line" lang="plaintext">Added info about cut command to output of help command.</span>
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3844
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3847
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<pre style="margin: 0;"> <span id="LC3847" class="line" lang="plaintext">.RE</span>
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3845
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3848
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<pre style="margin: 0;"> <span id="LC3848" class="line" lang="plaintext">.LP</span>
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3846
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3849
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<pre style="margin: 0;"> <span id="LC3849" class="line" lang="plaintext">.\" ============================================================================</span>
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<li id="b0109d980457466d1deec0f79c45e2b54114fdd5">
<a href="https://salsa.debian.org/med-team/vsearch/commit/8f9cb2d86c9d55fa125f18d7065bc4390550d5a2#b0109d980457466d1deec0f79c45e2b54114fdd5"><strong>src/vsearch.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4279,7 +4279,7 @@ void cmd_help()</td>
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4279
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4279
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<pre style="margin: 0;"> <span id="LC4279" class="line" lang="cpp"> <span class="s" style="color: #d14;">" Data</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num old_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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4280
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<pre style="margin: 0;"> <span id="LC4280" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --reverse FILENAME specify FASTQ file with reverse reads</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4281
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4281
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<pre style="margin: 0;"> <span id="LC4281" class="line" lang="cpp"> <span class="s" style="color: #d14;">" Parameters</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4282
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<pre style="margin: 0;">-<span id="LC4282" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastq_allowmergestagger <span class="idiff left right">A</span>llow merging of staggered reads</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4282
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<pre style="margin: 0;">+<span id="LC4282" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastq_allowmergestagger <span class="idiff left right">a</span>llow merging of staggered reads</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4283
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4283
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<pre style="margin: 0;"> <span id="LC4283" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastq_ascii INT FASTQ input quality score ASCII base char (33)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4284
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4284
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<pre style="margin: 0;"> <span id="LC4284" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastq_maxdiffpct REAL maximum percentage diff. bases in overlap (100.0)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4285
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4285
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<pre style="margin: 0;"> <span id="LC4285" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastq_maxdiffs INT maximum number of different bases in overlap (10)</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="4313" style="width: 35px; color: rgba(0,0,0,0.3); 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="4313" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4313,8 +4313,18 @@ void cmd_help()</td>
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4313
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4313
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<pre style="margin: 0;"> <span id="LC4313" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --alnout FILENAME filename for human-readable alignment output</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4314
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4314
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<pre style="margin: 0;"> <span id="LC4314" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --acceptall output all pairwise alignments</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4315
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4315
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<pre style="margin: 0;"> <span id="LC4315" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4316
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<pre style="margin: 0;">+<span id="LC4316" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Restriction site cutting</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4317
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<pre style="margin: 0;">+<span id="LC4317" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --cut FILENAME filename of FASTA formatted input sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4318
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<pre style="margin: 0;">+<span id="LC4318" class="line" lang="cpp"> <span class="s" style="color: #d14;">" Parameters</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4319
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<pre style="margin: 0;">+<span id="LC4319" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --cut_pattern STRING pattern to match with ^ and _ at cut sites</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4320
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<pre style="margin: 0;">+<span id="LC4320" class="line" lang="cpp"> <span class="s" style="color: #d14;">" Output</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4321
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<pre style="margin: 0;">+<span id="LC4321" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastaout FILENAME FASTA filename for fragments on forward strand</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4322
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<pre style="margin: 0;">+<span id="LC4322" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastaout_rev FILENAME FASTA filename for fragments on reverse strand</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4323
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<pre style="margin: 0;">+<span id="LC4323" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastaout_discarded FN FASTA filename for non-matching sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4324
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<pre style="margin: 0;">+<span id="LC4324" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastaout_discarded_rev FN FASTA filename for non-matching, reverse compl.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4325
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<pre style="margin: 0;">+<span id="LC4325" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4316
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<td class="diff-line-num new_line" data-linenumber="4326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4326
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<pre style="margin: 0;"> <span id="LC4326" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Reverse complementation</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4317
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<td class="diff-line-num new_line old" data-linenumber="4327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4317" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastx_revcomp FILENAME <span class="idiff left right">R</span>everse-complement seqs in FASTA or FASTQ file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4327
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<pre style="margin: 0;">+<span id="LC4327" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastx_revcomp FILENAME <span class="idiff left right">r</span>everse-complement seqs in FASTA or FASTQ file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4318
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4328
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<pre style="margin: 0;"> <span id="LC4328" class="line" lang="cpp"> <span class="s" style="color: #d14;">" Parameters</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4319
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4329
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<pre style="margin: 0;"> <span id="LC4329" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastq_ascii INT FASTQ input quality score ASCII base char (33)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4320
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4330
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<pre style="margin: 0;"> <span id="LC4330" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastq_qmax INT maximum base quality value for FASTQ input (41)</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="4322" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4322,7 +4332,7 @@ void cmd_help()</td>
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4322
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4332
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<pre style="margin: 0;"> <span id="LC4332" class="line" lang="cpp"> <span class="s" style="color: #d14;">" Output</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4323
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4333
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<pre style="margin: 0;"> <span id="LC4333" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastaout FILENAME FASTA output filename</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4324
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4334
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<pre style="margin: 0;"> <span id="LC4334" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --fastqout FILENAME FASTQ output filename</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4325
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<pre style="margin: 0;">-<span id="LC4325" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --label_suffix STRING <span class="idiff left right">L</span>abel to append to identifier in the 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 new old_line" data-linenumber="4326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4335
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<pre style="margin: 0;">+<span id="LC4335" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --label_suffix STRING <span class="idiff left right">l</span>abel to append to identifier in the 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 old_line" data-linenumber="4326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4326
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<td class="diff-line-num new_line" data-linenumber="4336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4336
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<pre style="margin: 0;"> <span id="LC4336" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num old_line" data-linenumber="4327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4327
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<td class="diff-line-num new_line" data-linenumber="4337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4337
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<pre style="margin: 0;"> <span id="LC4337" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Searching</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="4328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4328
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<td class="diff-line-num new_line" data-linenumber="4338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4338
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<pre style="margin: 0;"> <span id="LC4338" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --search_exact FILENAME filename of queries for exact match search</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="4670" style="width: 35px; color: rgba(0,0,0,0.3); 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="4680" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4670,6 +4680,7 @@ void cmd_none()</td>
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4670
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<td class="diff-line-num new_line" data-linenumber="4680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4680
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<pre style="margin: 0;"> <span id="LC4680" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num old_line" data-linenumber="4671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4671
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4681
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<pre style="margin: 0;"> <span id="LC4681" class="line" lang="cpp"> <span class="s" style="color: #d14;">"vsearch --allpairs_global FILENAME --id 0.5 --alnout FILENAME</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4672
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4682
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<pre style="margin: 0;"> <span id="LC4682" class="line" lang="cpp"> <span class="s" style="color: #d14;">"vsearch --cluster_size FILENAME --id 0.97 --centroids FILENAME</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="4673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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4683
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<pre style="margin: 0;">+<span id="LC4683" class="line" lang="cpp"> <span class="s" style="color: #d14;">"vsearch --cut FILENAME --cut_pattern G^AATT_C --fastaout FILENAME</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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4673
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<td class="diff-line-num new_line" data-linenumber="4684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4684
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<pre style="margin: 0;"> <span id="LC4684" class="line" lang="cpp"> <span class="s" style="color: #d14;">"vsearch --derep_fulllength FILENAME --output FILENAME</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="4674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4674
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<td class="diff-line-num new_line" data-linenumber="4685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4685
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<pre style="margin: 0;"> <span id="LC4685" class="line" lang="cpp"> <span class="s" style="color: #d14;">"vsearch --fastq_chars FILENAME</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="4675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4675
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<td class="diff-line-num new_line" data-linenumber="4686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4686
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<pre style="margin: 0;"> <span id="LC4686" class="line" lang="cpp"> <span class="s" style="color: #d14;">"vsearch --fastq_convert FILENAME --fastqout FILENAME --fastq_ascii 64</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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