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<h3>

Nilesh Patra pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/seqkit">Debian Med / seqkit</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4">5388a29b</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2022-01-16T18:15:51+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.0+ds</pre>

</li>

</ul>

<h4>23 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

<span class="deleted-file">

−

.travis.yml

</span>

</a>

</li>

<li class="file-stats">

<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">

CHANGELOG.md

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#7cdca301cbb4c2d5233c0eed1f6571d394148920">

doc/docs/download.md

</a>

</li>

<li class="file-stats">

<a href="#c47645c391ad0571c40779079363c9d48412e18b">

go.mod

</a>

</li>

<li class="file-stats">

<a href="#5aa1ac64de2b0c4821af9393b44965020e4a521d">

go.sum

</a>

</li>

<li class="file-stats">

<a href="#6aac2ac8b11e949fae92fe504b39efb74c521140">

seqkit/cmd/amplicon.go

</a>

</li>

<li class="file-stats">

<a href="#ac97d1d61f0fcd1ddb3fe8fe78c921e2456a4121">

seqkit/cmd/bam.go

</a>

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<li class="file-stats">

<a href="#9be4e7ddcb85159e03aeabe59c53722d78a29001">

seqkit/cmd/bed.go

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<li class="file-stats">

<a href="#1e70a04962951435ea946f5b302ca407674cf304">

seqkit/cmd/faidx.go

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<a href="#2bb8272102c7745e0c153fd1d33014c3a7fed384">

seqkit/cmd/fq2fa.go

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<li class="file-stats">

<a href="#76486b4b36e99fed87fd3aeff9124f70d282a3bc">

seqkit/cmd/fx2tab.go

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<li class="file-stats">

<a href="#a02b528e8138ab6ad3eae788206eb69181c130ba">

seqkit/cmd/grep.go

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<li class="file-stats">

<a href="#da9f919e44db345f43e899023ccde1e429864c15">

seqkit/cmd/locate.go

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<li class="file-stats">

<a href="#29fe4b7c1fedb5f9aec18990085490fee6564b10">

seqkit/cmd/mutate.go

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<li class="file-stats">

<a href="#604fd55a896e470ee80f4ea9caf71f879579d68c">

seqkit/cmd/pair.go

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<li class="file-stats">

<a href="#32f77b9b26ba8c525e818703d5ae667b751cebef">

seqkit/cmd/replace.go

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<li class="file-stats">

<a href="#fb73906bdb791ca7cb1138a6de00ba5ad4521465">

seqkit/cmd/root.go

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</li>

<li class="file-stats">

<a href="#f6639935f1c63a101930babdf188dc5db8749963">

seqkit/cmd/scat.go

</a>

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<li class="file-stats">

<a href="#1d415668e438829ee466a5e6b51f9c42ca064b0c">

seqkit/cmd/shuffle.go

</a>

</li>

<li class="file-stats">

<a href="#92b5b49951aa33ccf0a6d8b10622240cc64511e8">

seqkit/cmd/sort.go

</a>

</li>

<li class="file-stats">

<a href="#ecd9ca523ede3e6b5b35186b55d0ce7e3198e7c9">

seqkit/cmd/split.go

</a>

</li>

<li class="file-stats">

<a href="#08f4007a2dcdd77b75167cfe678d33d187bd0572">

tests/test.sh

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>

deleted

</a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">go</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml">  <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml">      <span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">bionic</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml">      <span class="na" style="color: #008080;">osx_image</span><span class="pi">:</span> <span class="s" style="color: #d14;">xcode10</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"><span class="na" style="color: #008080;">go</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">1.x</span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"><span class="na" style="color: #008080;">cache</span><span class="pi">:</span> <span class="s" style="color: #d14;">miniconda3</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"></span>

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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="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>

</pre>

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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;">if [ $TRAVIS_OS_NAME = "linux" ]; then wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [ $TRAVIS_OS_NAME = "osx" ]; then wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh; fi;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">bash ./miniconda.sh -u -b -p ./miniconda3 && source ./miniconda3/bin/activate;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">conda init bash && source $HOME/.bashrc;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">conda update -q --yes conda;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">conda update -q --yes --all;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">conda config --add channels conda-forge;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">conda config --add channels conda-forge;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">conda install -q --yes sed openssl;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml">    <span class="pi">-</span> <span class="s" style="color: #d14;">./tests/test.sh</span></span></pre>

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<br>

</li>

<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>

<hr>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">SeqKit v2.1.0</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/tag/v2.1.0</span><span class="p">)</span> - 2021-11-15</span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Release)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/v2.1.0/total.svg</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/tag/v2.1.0)</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">    -</span> <span class="sb" style="color: #d14;">`seqkit seq`</span>:</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">        -</span> <span class="gs" style="font-weight: 600;">**fix filtering by average quality `-Q/-R`**</span>. <span class="p">[</span><span class="nv" style="color: #008080;">#257</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/257</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">    -</span> <span class="sb" style="color: #d14;">`seqkit convert`</span>:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">        -</span> fix quality encoding checking, change default value of <span class="sb" style="color: #d14;">`-N/--thresh-B-in-n-most-common`</span> from <span class="sb" style="color: #d14;">`4`</span> to <span class="sb" style="color: #d14;">`2`</span>. </span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">        <span class="p">[</span><span class="nv" style="color: #008080;">#254</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/254</span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">#239</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/239]</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">    -</span> <span class="sb" style="color: #d14;">`seqkit split`</span>:</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">        -</span> fix writing an extra empty file when using <span class="sb" style="color: #d14;">`--two-pass`</span><span class="p">[</span><span class="nv" style="color: #008080;">#244</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/244</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">    -</span> <span class="sb" style="color: #d14;">`seqkit subseq`</span>:</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">        -</span> fix <span class="sb" style="color: #d14;">`--bed`</span> which fail to recognize strand <span class="sb" style="color: #d14;">`.`</span>.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p">    -</span> <span class="sb" style="color: #d14;">`seqkit fq2fa`</span>: </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="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">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">        -</span> faster, and do not wrap sequences.</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="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">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">    -</span> <span class="sb" style="color: #d14;">`seqkit grep/locate/mutate`</span>:</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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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="LC15" class="line" lang="markdown"><span class="p">        -</span> detect unquoted comma and show warning message, e.g., <span class="sb" style="color: #d14;">`-p 'A{2,}'`</span>. <span class="p">[</span><span class="nv" style="color: #008080;">#250</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/250</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">SeqKit v2.0.0</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/tag/v2.0.0</span><span class="p">)</span> - 2021-08-27</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Release)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/v2.0.0/total.svg</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/tag/v2.0.0)</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="p">    -</span> <span class="gs" style="font-weight: 600;">**Performance improvements**</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); 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="67" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -67,7 +67,7 @@ install via conda:</td>

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<td class="old_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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<td class="new_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown">|                 |<span class="p">[</span><span class="nv" style="color: #008080;">common</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bioinf.shenwei.me/seqkit/usage/#common</span><span class="p">)</span>           |find common sequences of multiple files by id/name/sequence                             |FASTA/Q        |+ and -           |             |               |</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

68

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<td class="new_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

68

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown">|                 |<span class="p">[</span><span class="nv" style="color: #008080;">duplicate</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bioinf.shenwei.me/seqkit/usage/#duplicate</span><span class="p">)</span>     |duplicate sequences N times                                                             |FASTA/Q        |                  |             |★              |</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

69

</td>

<td class="new_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

69

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown">|                 |<span class="p">[</span><span class="nv" style="color: #008080;">split</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bioinf.shenwei.me/seqkit/usage/#split</span><span class="p">)</span>             |split sequences into files by id/seq region/size/parts (mainly for FASTA)               |FASTA preffered|                  |             |★              |</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

70

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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(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="LC70" class="line" lang="markdown">|                 |<span class="p">[</span><span class="nv" style="color: #008080;">spit2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bioinf.shenwei.me/seqkit/usage/#spit2</span><span class="p">)</span>           <span class="idiff left right">  </span>|split sequences into files by size/parts (FASTA, PE/SE FASTQ)                           |FASTA/Q        |                  |             |★★             |</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

70

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown">|                 |<span class="p">[</span><span class="nv" style="color: #008080;">sp<span class="idiff left">l</span>it2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bioinf.shenwei.me/seqkit/usage/#sp<span class="idiff right">l</span>it2</span><span class="p">)</span>           |split sequences into files by size/parts (FASTA, PE/SE FASTQ)                           |FASTA/Q        |                  |             |★★             |</span>

</pre>

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71

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<td class="new_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(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="LC71" class="line" lang="markdown">|                 |<span class="p">[</span><span class="nv" style="color: #008080;">head</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bioinf.shenwei.me/seqkit/usage/#head</span><span class="p">)</span>               |print first N FASTA/Q records                                                           |FASTA/Q        |                  |             |               |</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

72

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown">|                 |<span class="p">[</span><span class="nv" style="color: #008080;">head-genome</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bioinf.shenwei.me/seqkit/usage/#head-genome</span><span class="p">)</span> |print sequences of the first genome with common prefixes in name                        |FASTA/Q        |                  |             |               |</span>

</pre>

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73

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown">|                 |<span class="p">[</span><span class="nv" style="color: #008080;">range</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bioinf.shenwei.me/seqkit/usage/#range</span><span class="p">)</span>             |print FASTA/Q records in a range (start:end)                                            |FASTA/Q        |                  |             |               |</span>

</pre>

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<br>

</li>

<li id="7cdca301cbb4c2d5233c0eed1f6571d394148920">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#7cdca301cbb4c2d5233c0eed1f6571d394148920"><strong>doc/docs/download.md</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,13 +9,13 @@ Please cite: **W Shen**, S Le, Y Li\*, F Hu\*. SeqKit: a cross-platform and ultr</td>

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9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>

</pre>

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10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown">OS     |Arch      |File, 中国镜像                                                                                                                                                                                  |Download Count</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown">:------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown">Linux  |32-bit    |<span class="p">[</span><span class="nv" style="color: #008080;">seqkit_linux_386.tar.gz</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">0</span>.0/seqkit_linux_386.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz</span><span class="p">)</span>                            |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">0</span>.0/seqkit_linux_386.tar.gz)</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown">Linux  |<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_linux_amd64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">0</span>.0/seqkit_linux_amd64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz</span><span class="p">)</span>                  |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">0</span>.0/seqkit_linux_amd64.tar.gz)</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown">Linux  |<span class="gs" style="font-weight: 600;">**arm64**</span> |<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_linux_arm64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">0</span>.0/seqkit_linux_arm64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz</span><span class="p">)</span>                  |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">0</span>.0/seqkit_linux_arm64.tar.gz)</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown">macOS  |<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_darwin_amd64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">0</span>.0/seqkit_darwin_amd64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz</span><span class="p">)</span>               |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">0</span>.0/seqkit_darwin_amd64.tar.gz)</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown">macOS  |<span class="gs" style="font-weight: 600;">**arm64**</span> |<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_darwin_arm64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">0</span>.0/seqkit_darwin_arm64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz</span><span class="p">)</span>               |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">0</span>.0/seqkit_darwin_arm64.tar.gz)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown">Windows|32-bit    |<span class="p">[</span><span class="nv" style="color: #008080;">seqkit_windows_386.exe.tar.gz</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">0</span>.0/seqkit_windows_386.exe.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz</span><span class="p">)</span>          |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">0</span>.0/seqkit_windows_386.exe.tar.gz)</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown">Windows|<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_windows_amd64.exe.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">0</span>.0/seqkit_windows_amd64.exe.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz</span><span class="p">)</span>|<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">0</span>.0/seqkit_windows_amd64.exe.tar.gz)</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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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="LC12" class="line" lang="markdown">Linux  |32-bit    |<span class="p">[</span><span class="nv" style="color: #008080;">seqkit_linux_386.tar.gz</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">1</span>.0/seqkit_linux_386.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz</span><span class="p">)</span>                            |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">1</span>.0/seqkit_linux_386.tar.gz)</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="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">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">Linux  |<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_linux_amd64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">1</span>.0/seqkit_linux_amd64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz</span><span class="p">)</span>                  |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">1</span>.0/seqkit_linux_amd64.tar.gz)</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="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">

14

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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="LC14" class="line" lang="markdown">Linux  |<span class="gs" style="font-weight: 600;">**arm64**</span> |<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_linux_arm64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">1</span>.0/seqkit_linux_arm64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz</span><span class="p">)</span>                  |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">1</span>.0/seqkit_linux_arm64.tar.gz)</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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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="LC15" class="line" lang="markdown">macOS  |<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_darwin_amd64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">1</span>.0/seqkit_darwin_amd64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz</span><span class="p">)</span>               |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">1</span>.0/seqkit_darwin_amd64.tar.gz)</span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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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="LC16" class="line" lang="markdown">macOS  |<span class="gs" style="font-weight: 600;">**arm64**</span> |<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_darwin_arm64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">1</span>.0/seqkit_darwin_arm64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz</span><span class="p">)</span>               |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">1</span>.0/seqkit_darwin_arm64.tar.gz)</span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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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="LC17" class="line" lang="markdown">Windows|32-bit    |<span class="p">[</span><span class="nv" style="color: #008080;">seqkit_windows_386.exe.tar.gz</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">1</span>.0/seqkit_windows_386.exe.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz</span><span class="p">)</span>          |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">1</span>.0/seqkit_windows_386.exe.tar.gz)</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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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="LC18" class="line" lang="markdown">Windows|<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_windows_amd64.exe.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff left">1</span>.0/seqkit_windows_amd64.exe.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz</span><span class="p">)</span>|<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v2.<span class="idiff right">1</span>.0/seqkit_windows_amd64.exe.tar.gz)</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Notes*</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"></span>

</pre>

</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">@@ -98,6 +98,21 @@ fish:</td>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Release History</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">SeqKit v2.1.0</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/tag/v2.1.0</span><span class="p">)</span> - 2021-11-15</span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Release)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/v2.1.0/total.svg</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/tag/v2.1.0)</span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"><span class="p">    -</span> <span class="sb" style="color: #d14;">`seqkit seq`</span>:</span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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">

104

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"><span class="p">        -</span> <span class="gs" style="font-weight: 600;">**fix filtering by average quality `-Q/-R`**</span>. <span class="p">[</span><span class="nv" style="color: #008080;">#257</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/257</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

105

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="p">    -</span> <span class="sb" style="color: #d14;">`seqkit convert`</span>:</span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"><span class="p">        -</span> fix quality encoding checking, change default value of <span class="sb" style="color: #d14;">`-N/--thresh-B-in-n-most-common`</span> from <span class="sb" style="color: #d14;">`4`</span> to <span class="sb" style="color: #d14;">`2`</span>. </span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC107" class="line" lang="markdown">        <span class="p">[</span><span class="nv" style="color: #008080;">#254</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/254</span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">#239</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/239]</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC108" class="line" lang="markdown"><span class="p">    -</span> <span class="sb" style="color: #d14;">`seqkit split`</span>:</span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"><span class="p">        -</span> fix writing an extra empty file when using <span class="sb" style="color: #d14;">`--two-pass`</span><span class="p">[</span><span class="nv" style="color: #008080;">#244</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/244</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"><span class="p">    -</span> <span class="sb" style="color: #d14;">`seqkit subseq`</span>:</span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown"><span class="p">        -</span> fix <span class="sb" style="color: #d14;">`--bed`</span> which fail to recognize strand <span class="sb" style="color: #d14;">`.`</span>.</span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

112

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"><span class="p">    -</span> <span class="sb" style="color: #d14;">`seqkit fq2fa`</span>: </span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

113

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"><span class="p">        -</span> faster, and do not wrap sequences.</span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"><span class="p">    -</span> <span class="sb" style="color: #d14;">`seqkit grep/locate/mutate`</span>:</span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"><span class="p">        -</span> detect unquoted comma and show warning message, e.g., <span class="sb" style="color: #d14;">`-p 'A{2,}'`</span>. <span class="p">[</span><span class="nv" style="color: #008080;">#250</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/250</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(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="LC116" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">SeqKit v2.0.0</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/tag/v2.0.0</span><span class="p">)</span> - 2021-08-27</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Release)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/v2.0.0/total.svg</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/tag/v2.0.0)</span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"><span class="p">    -</span> <span class="gs" style="font-weight: 600;">**Performance improvements**</span></span>

</pre>

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<br>

</li>

<li id="c47645c391ad0571c40779079363c9d48412e18b">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#c47645c391ad0571c40779079363c9d48412e18b"><strong>go.mod</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,15 +13,15 @@ require (</td>

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/iafan/cwalk@v0.0.0-20210125030640-586a8832a711" rel="nofollow noreferrer noopener" target="_blank">github.com/iafan/cwalk</a> v0.0.0-20210125030640-586a8832a711</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/klauspost/pgzip@v1.2.5" rel="nofollow noreferrer noopener" target="_blank">github.com/klauspost/pgzip</a> v1.2.5</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/logrusorgru/aurora@v2.0.3+incompatible" rel="nofollow noreferrer noopener" target="_blank">github.com/logrusorgru/aurora</a> v2.0.3+incompatible</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="new_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/mattn/go-colorable@v0.1.8" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-colorable</a> v0.1.<span class="idiff left right">8</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

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<td class="new_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/mattn/go-isatty@v0.0.13" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-isatty</a> v0.0.1<span class="idiff left right">3</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC16" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/mattn/go-colorable@v0.1.11" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-colorable</a> v0.1.<span class="idiff left right">11</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/mattn/go-isatty@v0.0.14" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-isatty</a> v0.0.1<span class="idiff left right">4</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/mitchellh/go-homedir@v1.1.0" rel="nofollow noreferrer noopener" target="_blank">github.com/mitchellh/go-homedir</a> v1.1.0</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/pkg/errors@v0.9.1" rel="nofollow noreferrer noopener" target="_blank">github.com/pkg/errors</a> v0.9.1</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/shenwei356/bio@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bio</a> v0.<span class="idiff left right">3.1</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC20" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/shenwei356/bio@v0.6.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bio</a> v0.<span class="idiff left right">6.0</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(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="LC21" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/shenwei356/breader@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/breader</a> v0.3.1</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/shenwei356/bwt@v0.5.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bwt</a> v0.5.1</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(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="LC23" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/shenwei356/go-logging@v0.0.0-20171012171522-c6b9702d88ba" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/go-logging</a> v0.0.0-20171012171522-c6b9702d88ba</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

24

</td>

<td class="new_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/shenwei356/util@v0.3.2" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/util</a> v0.<span class="idiff left right">3.2</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC24" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/shenwei356/util@v0.5.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/util</a> v0.<span class="idiff left right">5.0</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

</td>

<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(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="LC25" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/shenwei356/xopen@v0.1.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/xopen</a> v0.1.0</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

26

</td>

<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/smallfish/simpleyaml@v0.1.0" rel="nofollow noreferrer noopener" target="_blank">github.com/smallfish/simpleyaml</a> v0.1.0</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

</td>

<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(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="LC27" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/spf13/cobra@v1.2.1" rel="nofollow noreferrer noopener" target="_blank">github.com/spf13/cobra</a> v1.2.1</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="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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,12 +39,11 @@ require (</td>

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<td class="old_line diff-line-num" 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">

39

</td>

<td class="new_line diff-line-num" 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">

39

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/klauspost/compress@v1.13.6" rel="nofollow noreferrer noopener" target="_blank">github.com/klauspost/compress</a> v1.13.6 // indirect</span>

</pre>

</td>

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<td class="old_line diff-line-num" 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">

40

</td>

<td class="new_line diff-line-num" 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">

40

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/mattn/go-runewidth@v0.0.13" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-runewidth</a> v0.0.13 // indirect</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

</td>

<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(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="LC41" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/rivo/uniseg@v0.2.0" rel="nofollow noreferrer noopener" target="_blank">github.com/rivo/uniseg</a> v0.2.0 // indirect</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

42

</td>

<td class="new_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(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="LC42" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/shenwei356/bpool@v0.0.0-20160710042833-f9e0ee4d0403" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bpool</a> v0.0.0-20160710042833-f9e0ee4d0403 // indirect</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

</td>

<td class="new_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/shenwei356/natsort@v0.0.0-20190418160752-600d539c017d" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/natsort</a> v0.0.0-20190418160752-600d539c017d // indirect</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

</td>

<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">     <a href="https://pkg.go.dev/github.com/spf13/pflag@v1.0.5" rel="nofollow noreferrer noopener" target="_blank">github.com/spf13/pflag</a> v1.0.5 // indirect</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

</td>

<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">     <a href="https://pkg.go.dev/golang.org/x/crypto@v0.0.0-20200622213623-75b288015ac9" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/crypto</a> v0.0.0-20200622213623-75b288015ac9 // indirect</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

</td>

<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">     <a href="https://pkg.go.dev/golang.org/x/image@v0.0.0-20190802002840-cff245a6509b" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/image</a> v0.0.0-20190802002840-cff245a6509b // indirect</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

47

</td>

<td class="new_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(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="LC47" class="line" lang="plaintext">     <a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20210630005230-0f9fa26af87c" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20210<span class="idiff left right">630005230-0f9fa26af87c</span> // indirect</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

46

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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="LC46" class="line" lang="plaintext">     <a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20210927094055-39ccf1dd6fa6" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20210<span class="idiff left right">927094055-39ccf1dd6fa6</span> // indirect</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

48

</td>

<td class="new_line diff-line-num" 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">

47

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">     <a href="https://pkg.go.dev/gonum.org/v1/plot@v0.0.0-20190515093506-e2840ee46a6b" rel="nofollow noreferrer noopener" target="_blank">gonum.org/v1/plot</a> v0.0.0-20190515093506-e2840ee46a6b // indirect</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

</td>

<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

48

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">     <a href="https://pkg.go.dev/gopkg.in/yaml.v2@v2.4.0" rel="nofollow noreferrer noopener" target="_blank">gopkg.in/yaml.v2</a> v2.4.0 // indirect</span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">)</span></pre>

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<li id="5aa1ac64de2b0c4821af9393b44965020e4a521d">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#5aa1ac64de2b0c4821af9393b44965020e4a521d"><strong>go.sum</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -217,12 +217,11 @@ github.com/logrusorgru/aurora v2.0.3+incompatible h1:tOpm7WcpBTn4fjmVfgpQq0EfczG</td>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/logrusorgru/aurora@v2.0.3+incompatible" rel="nofollow noreferrer noopener" target="_blank">github.com/logrusorgru/aurora</a> v2.0.3+incompatible/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/logrusorgru/aurora@v2.0.3+incompatible" rel="nofollow noreferrer noopener" target="_blank">7rIyQOR62GCctdiQpZ/zOJlFyk6y+94wXzv6RNZgaR4=</a></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/magiconair/properties@v1.8.5" rel="nofollow noreferrer noopener" target="_blank">github.com/magiconair/properties</a> v1.8.5/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/magiconair/properties@v1.8.5" rel="nofollow noreferrer noopener" target="_blank">y3VJvCyxH9uVvJTWEGAELF3aiYNyPKd5NZ3oSwXrF60=</a></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/mattn/go-colorable@v0.0.9" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-colorable</a> v0.0.9/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/mattn/go-colorable@v0.0.9" rel="nofollow noreferrer noopener" target="_blank">9vuHe8Xs5qXnSaW/c/ABM9alt+Vo+STaOChaDxuIBZU=</a></span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/mattn/go-colorable@v0.1.8" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-colorable</a> v0.1.<span class="idiff left">8</span> h1:<a href="https://sum.golang.org/lookup/github.com/mattn/go-colorable@v0.1.8" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">c1ghPdyEDarC70ftn0y+A/Ee++9zz8ljHG1b13eJ0s8</span>=</a></span>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/mattn/go-colorable@v0.1.8" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-colorable</a> v0.1.<span class="idiff left">8</span>/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/mattn/go-colorable@v0.1.8" rel="nofollow noreferrer noopener" target="_blank">u<span class="idiff right">6P/XSegPjTcexA+o6vUJrdnUu04hMope9wVRipJSqc</span>=</a></span>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/mattn/go-colorable@v0.1.11" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-colorable</a> v0.1.<span class="idiff left">11</span> h1:<a href="https://sum.golang.org/lookup/github.com/mattn/go-colorable@v0.1.11" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">nQ+aFkoE2TMGc0b68U2OKSexC+eq46+XwZzWXHRmPYs</span>=</a></span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/mattn/go-colorable@v0.1.11" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-colorable</a> v0.1.<span class="idiff left">11</span>/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/mattn/go-colorable@v0.1.11" rel="nofollow noreferrer noopener" target="_blank">u<span class="idiff right">5H1YNBxpqRaxsYJYSkiCWKzEfiAb1Gb520KVy5xxl4</span>=</a></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/mattn/go-isatty@v0.0.3" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-isatty</a> v0.0.3/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/mattn/go-isatty@v0.0.3" rel="nofollow noreferrer noopener" target="_blank">M+lRXTBqGeGNdLjl/ufCoiOlB5xdOkqRJdNxMWT7Zi4=</a></span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/mattn/go-isatty@v0.0.12" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-isatty</a> v0.0.12/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/mattn/go-isatty@v0.0.12" rel="nofollow noreferrer noopener" target="_blank">cbi8OIDigv2wuxKPP5vlRcQ1OAZbq2CE4Kysco4FUpU=</a></span>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/mattn/go-isatty@v0.0.13" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-isatty</a> v0.0.13 h1:<a href="https://sum.golang.org/lookup/github.com/mattn/go-isatty@v0.0.13" rel="nofollow noreferrer noopener" target="_blank">qdl+GuBjcsKKDco5BsxPJlId98mSWNKqYA+Co0SC1yA=</a></span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/mattn/go-isatty@v0.0.13" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-isatty</a> v0.0.13/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/mattn/go-isatty@v0.0.13" rel="nofollow noreferrer noopener" target="_blank">cbi8OIDigv2wuxKPP5vlRcQ1OAZbq2CE4Kysco4FUpU=</a></span>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/mattn/go-isatty@v0.0.14" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-isatty</a> v0.0.14 h1:<a href="https://sum.golang.org/lookup/github.com/mattn/go-isatty@v0.0.14" rel="nofollow noreferrer noopener" target="_blank">yVuAays6BHfxijgZPzw+3Zlu5yQgKGP2/hcQbHb7S9Y=</a></span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/mattn/go-isatty@v0.0.14" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-isatty</a> v0.0.14/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/mattn/go-isatty@v0.0.14" rel="nofollow noreferrer noopener" target="_blank">7GGIvUiUoEMVVmxf/4nioHXj79iQHKdU27kJ6hsGG94=</a></span>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/mattn/go-runewidth@v0.0.13" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-runewidth</a> v0.0.13 h1:<a href="https://sum.golang.org/lookup/github.com/mattn/go-runewidth@v0.0.13" rel="nofollow noreferrer noopener" target="_blank">lTGmDsbAYt5DmK6OnoV7EuIF1wEIFAcxld6ypU4OSgU=</a></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/mattn/go-runewidth@v0.0.13" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-runewidth</a> v0.0.13/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/mattn/go-runewidth@v0.0.13" rel="nofollow noreferrer noopener" target="_blank">Jdepj2loyihRzMpdS35Xk/zdY8IAYHsh153qUoGf23w=</a></span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/miekg/dns@v1.0.14" rel="nofollow noreferrer noopener" target="_blank">github.com/miekg/dns</a> v1.0.14/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/miekg/dns@v1.0.14" rel="nofollow noreferrer noopener" target="_blank">W1PPwlIAgtquWBMBEV9nkV9Cazfe8ScdGz/Lj7v3Nrg=</a></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); 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="238" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -239,6 +238,7 @@ github.com/mitchellh/mapstructure v1.4.1/go.mod h1:bFUtVrKA4DC2yAKiSyO/QUcy7e+RR</td>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/modern-go/concurrent@v0.0.0-20180228061459-e0a39a4cb421" rel="nofollow noreferrer noopener" target="_blank">github.com/modern-go/concurrent</a> v0.0.0-20180228061459-e0a39a4cb421/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/modern-go/concurrent@v0.0.0-20180228061459-e0a39a4cb421" rel="nofollow noreferrer noopener" target="_blank">6dJC0mAP4ikYIbvyc7fijjWJddQyLn8Ig3JB5CqoB9Q=</a></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/modern-go/reflect2@v0.0.0-20180701023420-4b7aa43c6742" rel="nofollow noreferrer noopener" target="_blank">github.com/modern-go/reflect2</a> v0.0.0-20180701023420-4b7aa43c6742/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/modern-go/reflect2@v0.0.0-20180701023420-4b7aa43c6742" rel="nofollow noreferrer noopener" target="_blank">bx2lNnkwVCuqBIxFjflWJWanXIb3RllmbCylyMrvgv0=</a></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/modern-go/reflect2@v1.0.1" rel="nofollow noreferrer noopener" target="_blank">github.com/modern-go/reflect2</a> v1.0.1/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/modern-go/reflect2@v1.0.1" rel="nofollow noreferrer noopener" target="_blank">bx2lNnkwVCuqBIxFjflWJWanXIb3RllmbCylyMrvgv0=</a></span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/montanaflynn/stats@v0.6.6" rel="nofollow noreferrer noopener" target="_blank">github.com/montanaflynn/stats</a> v0.6.6/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/montanaflynn/stats@v0.6.6" rel="nofollow noreferrer noopener" target="_blank">etXPPgVO6n31NxCd9KQUMvCM+ve0ruNzt6R8Bnaayow=</a></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/pascaldekloe/goe@v0.0.0-20180627143212-57f6aae5913c" rel="nofollow noreferrer noopener" target="_blank">github.com/pascaldekloe/goe</a> v0.0.0-20180627143212-57f6aae5913c/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/pascaldekloe/goe@v0.0.0-20180627143212-57f6aae5913c" rel="nofollow noreferrer noopener" target="_blank">lzWF7FIEvWOWxwDKqyGYQf6ZUaNfKdP144TG7ZOy1lc=</a></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/pelletier/go-toml@v1.9.3" rel="nofollow noreferrer noopener" target="_blank">github.com/pelletier/go-toml</a> v1.9.3/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/pelletier/go-toml@v1.9.3" rel="nofollow noreferrer noopener" target="_blank">u1nR/EPcESfeI/szUZKdtJ0xRNbUoANCkoOuaOx1Y+c=</a></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/pkg/errors@v0.8.1" rel="nofollow noreferrer noopener" target="_blank">github.com/pkg/errors</a> v0.8.1/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/pkg/errors@v0.8.1" rel="nofollow noreferrer noopener" target="_blank">bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=</a></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); 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="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/russross/blackfriday/v2@v2.0.1" rel="nofollow noreferrer noopener" target="_blank">github.com/russross/blackfriday/v2</a> v2.0.1/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/russross/blackfriday/v2@v2.0.1" rel="nofollow noreferrer noopener" target="_blank">+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=</a></span>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/ryanuber/columnize@v0.0.0-20160712163229-9b3edd62028f" rel="nofollow noreferrer noopener" target="_blank">github.com/ryanuber/columnize</a> v0.0.0-20160712163229-9b3edd62028f/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/ryanuber/columnize@v0.0.0-20160712163229-9b3edd62028f" rel="nofollow noreferrer noopener" target="_blank">sm1tb6uqfes/u+d4ooFouqFdy9/2g9QGwK3SQygK0Ts=</a></span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/sean-/seed@v0.0.0-20170313163322-e2103e2c3529" rel="nofollow noreferrer noopener" target="_blank">github.com/sean-/seed</a> v0.0.0-20170313163322-e2103e2c3529/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/sean-/seed@v0.0.0-20170313163322-e2103e2c3529" rel="nofollow noreferrer noopener" target="_blank">DxrIzT+xaE7yg65j358z/aeFdxmN0P9QXhEzd20vsDc=</a></span>

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bio@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bio</a> v0.3.1 h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bio@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">rdSoslv8HahfJpkzhN6W1Ky1lQ++gaBIfuJAC4f65cc=</a></span>

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<pre style="margin: 0;">-<span id="LC262" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bio@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bio</a> v0.3.1/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bio@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">rHA8DoaDooXKdqX7bqoksQDKm3mEAQ3MsD9nivVTSf0=</a></span>

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<pre style="margin: 0;">-<span id="LC263" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bpool@v0.0.0-20160710042833-f9e0ee4d0403" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bpool</a> v0.0.0-20160710042833-f9e0ee4d0403 h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bpool@v0.0.0-20160710042833-f9e0ee4d0403" rel="nofollow noreferrer noopener" target="_blank">/3JklLnHXiWUBxWc3joQYavDQJpncRhRA909cUb7eOw=</a></span>

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<pre style="margin: 0;">-<span id="LC264" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bpool@v0.0.0-20160710042833-f9e0ee4d0403" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bpool</a> v0.0.0-20160710042833-f9e0ee4d0403/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bpool@v0.0.0-20160710042833-f9e0ee4d0403" rel="nofollow noreferrer noopener" target="_blank">YkgdTWfNnJgv5HVJbVSDmxQtkK3/jZWDoqcG26BVU8k=</a></span>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bio@v0.6.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bio</a> v0.6.0 h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bio@v0.6.0" rel="nofollow noreferrer noopener" target="_blank">od1J1/tpXZ5p6DiPa5kCM+ijl1uesSmndhmZkirnglE=</a></span>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bio@v0.6.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bio</a> v0.6.0/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bio@v0.6.0" rel="nofollow noreferrer noopener" target="_blank">LL8JBeJnKQ4esixngQZiTkZgO1/by1qI0XhMrUl7T8M=</a></span>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/breader@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/breader</a> v0.3.1 h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/breader@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">OjgfeHhpNGQPkS1+lgsl4eNuuO//Y16N6TkqG5oxO5U=</a></span>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/breader@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/breader</a> v0.3.1/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/breader@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">UR11JJCxU9s7eUdU4xn3L/VodxoXzWhjJPh8WZbb+us=</a></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bwt@v0.5.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bwt</a> v0.5.1 h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bwt@v0.5.1" rel="nofollow noreferrer noopener" target="_blank">pq9KxkJPwzUwPjwWqfTOkUmzwHm8JtMkZxBkqkzuIVo=</a></span>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bwt@v0.5.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bwt</a> v0.5.1/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bwt@v0.5.1" rel="nofollow noreferrer noopener" target="_blank">V2hX4adhr4WfFpy2ogKiV8A2WO9FeK0wkq1o3/R91mE=</a></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/go-logging@v0.0.0-20171012171522-c6b9702d88ba" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/go-logging</a> v0.0.0-20171012171522-c6b9702d88ba h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/go-logging@v0.0.0-20171012171522-c6b9702d88ba" rel="nofollow noreferrer noopener" target="_blank">UvnrxFDPmz7agYX0eQ2JEorTKn1ORnZ9dT5OzbjPvK8=</a></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/go-logging@v0.0.0-20171012171522-c6b9702d88ba" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/go-logging</a> v0.0.0-20171012171522-c6b9702d88ba/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/go-logging@v0.0.0-20171012171522-c6b9702d88ba" rel="nofollow noreferrer noopener" target="_blank">LiqYp/K5yCEWOi7Ux/iOF/kjDxtsdYjOGcKHDbEOXFU=</a></span>

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/kmers@v0.1.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/kmers</a> v0.1.0/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/kmers@v0.1.0" rel="nofollow noreferrer noopener" target="_blank">23Ltr95n98LYy9OtJMFSzkmU/1nmdYwgzqB3walAQ6g=</a></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/natsort@v0.0.0-20190418160752-600d539c017d" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/natsort</a> v0.0.0-20190418160752-600d539c017d h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/natsort@v0.0.0-20190418160752-600d539c017d" rel="nofollow noreferrer noopener" target="_blank">eeXLHcXyGEr72V1SOSEI7vSzUOTJvHutwF7Ykm+hscQ=</a></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/natsort@v0.0.0-20190418160752-600d539c017d" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/natsort</a> v0.0.0-20190418160752-600d539c017d/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/natsort@v0.0.0-20190418160752-600d539c017d" rel="nofollow noreferrer noopener" target="_blank">SiiGiRFyRtV7S9RamOrmQR5gpGIRhWJM1w0EtmuQ1io=</a></span>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/util@v0.3.2" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/util</a> v0.<span class="idiff left">3.2</span> h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/util@v0.3.2" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">3qXkcO2erNKnPCnV8zxjN2JL5sGnOqW+muj1x4XxkuM</span>=</a></span>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/util@v0.3.2" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/util</a> v0.<span class="idiff left">3.2</span>/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/util@v0.3.2" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">pY/f5wR/0o0dJcodhw1Df/ghzqNt2wFSATW0zymI4mA</span>=</a></span>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/util@v0.5.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/util</a> v0.<span class="idiff left">5.0</span> h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/util@v0.5.0" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">gbPuGYVggNLOSORuZLnpaB2DrIpyDFolHiZQkyja+XU</span>=</a></span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/util@v0.5.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/util</a> v0.<span class="idiff left">5.0</span>/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/util@v0.5.0" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">goFN/u2HgvfbOsEgoHA2hUEet+9KjZpRavrVGz9cm30</span>=</a></span>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/xopen@v0.1.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/xopen</a> v0.1.0 h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/xopen@v0.1.0" rel="nofollow noreferrer noopener" target="_blank">PizY52rLA7A6EdkwKZ6A8h8/a+c9DCBXqfLtwVzsWnM=</a></span>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/zeebo/wyhash@v0.0.1" rel="nofollow noreferrer noopener" target="_blank">github.com/zeebo/wyhash</a> v0.0.1/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/zeebo/wyhash@v0.0.1" rel="nofollow noreferrer noopener" target="_blank">Ti+OwfNtM5AZiYAL0kOPIfliqDP5c0VtOnnMAqzuuZk=</a></span>

</pre>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="plaintext"><a href="https://pkg.go.dev/go.etcd.io/etcd/api/v3@v3.5.0" rel="nofollow noreferrer noopener" target="_blank">go.etcd.io/etcd/api/v3</a> v3.5.0/go.mod h1:<a href="https://sum.golang.org/lookup/go.etcd.io/etcd/api/v3@v3.5.0" rel="nofollow noreferrer noopener" target="_blank">cbVKeC6lCfl7j/8jBhAK6aIYO9XOjdptoxU/nLQcPvs=</a></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="plaintext"><a href="https://pkg.go.dev/go.etcd.io/etcd/client/pkg/v3@v3.5.0" rel="nofollow noreferrer noopener" target="_blank">go.etcd.io/etcd/client/pkg/v3</a> v3.5.0/go.mod h1:<a href="https://sum.golang.org/lookup/go.etcd.io/etcd/client/pkg/v3@v3.5.0" rel="nofollow noreferrer noopener" target="_blank">IJHfcCEKxYu1Os13ZdwCwIUTUVGYTSAM3YSwc9/Ac1g=</a></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="plaintext"><a href="https://pkg.go.dev/go.etcd.io/etcd/client/v2@v2.305.0" rel="nofollow noreferrer noopener" target="_blank">go.etcd.io/etcd/client/v2</a> v2.305.0/go.mod h1:<a href="https://sum.golang.org/lookup/go.etcd.io/etcd/client/v2@v2.305.0" rel="nofollow noreferrer noopener" target="_blank">h9puh54ZTgAKtEbut2oe9P4L/oqKCVB6xsXlzd7alYQ=</a></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); 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="445" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -444,7 +445,6 @@ golang.org/x/sys v0.0.0-20191005200804-aed5e4c7ecf9/go.mod h1:h1NjWce9XRLGQEsW7w</td>

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<pre style="margin: 0;"> <span id="LC445" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20191204072324-ce4227a45e2e" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20191204072324-ce4227a45e2e/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20191204072324-ce4227a45e2e" rel="nofollow noreferrer noopener" target="_blank">h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=</a></span>

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<pre style="margin: 0;"> <span id="LC446" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20191228213918-04cbcbbfeed8" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20191228213918-04cbcbbfeed8/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20191228213918-04cbcbbfeed8" rel="nofollow noreferrer noopener" target="_blank">h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=</a></span>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20200113162924-86b910548bc1" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20200113162924-86b910548bc1/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20200113162924-86b910548bc1" rel="nofollow noreferrer noopener" target="_blank">h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=</a></span>

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<pre style="margin: 0;">-<span id="LC447" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20200116001909-b77594299b42" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20200116001909-b77594299b42/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20200116001909-b77594299b42" rel="nofollow noreferrer noopener" target="_blank">h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=</a></span>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20200122134326-e047566fdf82" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20200122134326-e047566fdf82/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20200122134326-e047566fdf82" rel="nofollow noreferrer noopener" target="_blank">h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=</a></span>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20200202164722-d101bd2416d5" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20200202164722-d101bd2416d5/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20200202164722-d101bd2416d5" rel="nofollow noreferrer noopener" target="_blank">h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=</a></span>

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<pre style="margin: 0;"> <span id="LC450" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20200212091648-12a6c2dcc1e4" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20200212091648-12a6c2dcc1e4/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20200212091648-12a6c2dcc1e4" rel="nofollow noreferrer noopener" target="_blank">h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=</a></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); 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="470" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -470,8 +470,9 @@ golang.org/x/sys v0.0.0-20210320140829-1e4c9ba3b0c4/go.mod h1:h1NjWce9XRLGQEsW7w</td>

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<pre style="margin: 0;"> <span id="LC470" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20210330210617-4fbd30eecc44" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20210330210617-4fbd30eecc44/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20210330210617-4fbd30eecc44" rel="nofollow noreferrer noopener" target="_blank">h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=</a></span>

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20210403161142-5e06dd20ab57" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20210403161142-5e06dd20ab57/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20210403161142-5e06dd20ab57" rel="nofollow noreferrer noopener" target="_blank">h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=</a></span>

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20210510120138-977fb7262007" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20210510120138-977fb7262007/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20210510120138-977fb7262007" rel="nofollow noreferrer noopener" target="_blank">oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=</a></span>

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<pre style="margin: 0;">-<span id="LC473" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20210630005230-0f9fa26af87c" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20210630005230-0f9fa26af87c h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20210630005230-0f9fa26af87c" rel="nofollow noreferrer noopener" target="_blank">F1jZWGFhYfh0Ci55sIpILtKKK8p3i2/krTr0H1rg74I=</a></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

474

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20210630005230-0f9fa26af87c" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20210630005230-0f9fa26af87c/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20210630005230-0f9fa26af87c" rel="nofollow noreferrer noopener" target="_blank">oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=</a></span>

</pre>

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<pre style="margin: 0;">+<span id="LC474" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20210927094055-39ccf1dd6fa6" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20210927094055-39ccf1dd6fa6 h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20210927094055-39ccf1dd6fa6" rel="nofollow noreferrer noopener" target="_blank">foEbQz/B0Oz6YIqu/69kfXPYeFQAuuMYFkjaqXzl5Wo=</a></span>

</pre>

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/sys@v0.0.0-20210927094055-39ccf1dd6fa6" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/sys</a> v0.0.0-20210927094055-39ccf1dd6fa6/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/sys@v0.0.0-20210927094055-39ccf1dd6fa6" rel="nofollow noreferrer noopener" target="_blank">oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=</a></span>

</pre>

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475

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<pre style="margin: 0;"> <span id="LC476" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/term@v0.0.0-20201126162022-7de9c90e9dd1" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/term</a> v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/term@v0.0.0-20201126162022-7de9c90e9dd1" rel="nofollow noreferrer noopener" target="_blank">bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo=</a></span>

</pre>

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<pre style="margin: 0;"> <span id="LC477" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/text@v0.0.0-20170915032832-14c0d48ead0c" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/text</a> v0.0.0-20170915032832-14c0d48ead0c/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/text@v0.0.0-20170915032832-14c0d48ead0c" rel="nofollow noreferrer noopener" target="_blank">NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=</a></span>

</pre>

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<pre style="margin: 0;"> <span id="LC478" class="line" lang="plaintext"><a href="https://pkg.go.dev/golang.org/x/text@v0.3.0" rel="nofollow noreferrer noopener" target="_blank">golang.org/x/text</a> v0.3.0/go.mod h1:<a href="https://sum.golang.org/lookup/golang.org/x/text@v0.3.0" rel="nofollow noreferrer noopener" target="_blank">NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=</a></span>

</pre>

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</li>

<li id="6aac2ac8b11e949fae92fe504b39efb74c521140">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#6aac2ac8b11e949fae92fe504b39efb74c521140"><strong>seqkit/cmd/amplicon.go</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); 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="52" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -52,7 +52,7 @@ var ampliconCmd = &cobra.Command{</td>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="go"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="go"><span class="s" style="color: #d14;">Attentions:</span></span>

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<td class="old_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(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="LC54" class="line" lang="go"><span class="s" style="color: #d14;">  1. Only one (the longest) matching location is returned for every primer pair.</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

55

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="go"><span class="s" style="color: #d14;">  2. Mismatch is allowed, but the mismatch location (5' or 3') is not controled.<span class="idiff left right"> </span></span></span>

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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC55" class="line" lang="go"><span class="s" style="color: #d14;">  2. Mismatch is allowed, but the mismatch location (5' or 3') is not control<span class="idiff left right">l</span>ed.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(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="LC56" class="line" lang="go"><span class="s" style="color: #d14;">     You can increase the value of "-j/--threads" to accelerate processing.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

57

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<td class="new_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(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="LC57" class="line" lang="go"><span class="s" style="color: #d14;">  3. Degenerate bases/residues like "RYMM.." are also supported.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

58

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<td class="new_line diff-line-num" data-linenumber="58" style="width: 35px; color: rgba(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="LC58" class="line" lang="go"><span class="s" style="color: #d14;">     But do not use degenerate bases/residues in regular expression, you need</span></span>

</pre>

</td>

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<br>

</li>

<li id="ac97d1d61f0fcd1ddb3fe8fe78c921e2456a4121">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#ac97d1d61f0fcd1ddb3fe8fe78c921e2456a4121"><strong>seqkit/cmd/bam.go</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -707,14 +707,14 @@ var bamCmd = &cobra.Command{</td>

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707

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<pre style="margin: 0;"> <span id="LC707" class="line" lang="go">           <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="708" style="width: 35px; color: rgba(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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708

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<pre style="margin: 0;"> <span id="LC708" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

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<td class="new_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(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="LC709" class="line" lang="go">           <span class="n" style="color: #333;">fmap</span><span class="p">[</span><span class="s" style="color: #d14;">"RefAln"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fieldInfo</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

710

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<td class="new_line diff-line-num old" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC710" class="line" lang="go">                   <span class="s" style="color: #d14;">"Aligned refence length"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC710" class="line" lang="go">                   <span class="s" style="color: #d14;">"Aligned refe<span class="idiff left right">re</span>nce length"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

711

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<pre style="margin: 0;"> <span id="LC711" class="line" lang="go">                   <span class="k" style="font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Record</span><span class="p">)</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span> <span class="p">{</span></span>

</pre>

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712

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<td class="new_line diff-line-num" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

712

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<pre style="margin: 0;"> <span id="LC712" class="line" lang="go">                           <span class="k" style="font-weight: 600;">return</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Len</span><span class="p">())</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

713

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<td class="new_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

713

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<pre style="margin: 0;"> <span id="LC713" class="line" lang="go">                   <span class="p">},</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

714

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<td class="new_line diff-line-num" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

714

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<pre style="margin: 0;"> <span id="LC714" class="line" lang="go">           <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

715

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<td class="new_line diff-line-num" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

715

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<pre style="margin: 0;"> <span id="LC715" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

716

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<td class="new_line diff-line-num" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

716

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<pre style="margin: 0;"> <span id="LC716" class="line" lang="go">           <span class="n" style="color: #333;">fmap</span><span class="p">[</span><span class="s" style="color: #d14;">"RefCov"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fieldInfo</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

717

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<td class="new_line diff-line-num old" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC717" class="line" lang="go">                   <span class="s" style="color: #d14;">"Refence coverage"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC717" class="line" lang="go">                   <span class="s" style="color: #d14;">"Refe<span class="idiff left right">re</span>nce coverage"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

718

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC718" class="line" lang="go">                   <span class="k" style="font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Record</span><span class="p">)</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

719

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<td class="new_line diff-line-num" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

719

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<pre style="margin: 0;"> <span id="LC719" class="line" lang="go">                           <span class="k" style="font-weight: 600;">return</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Len</span><span class="p">())</span> <span class="o" style="font-weight: 600;">/</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Len</span><span class="p">())</span> <span class="o" style="font-weight: 600;">*</span> <span class="m" style="color: #099;">100</span></span>

</pre>

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720

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<td class="new_line diff-line-num" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

720

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<pre style="margin: 0;"> <span id="LC720" class="line" lang="go">                   <span class="p">},</span></span>

</pre>

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<br>

</li>

<li id="9be4e7ddcb85159e03aeabe59c53722d78a29001">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#9be4e7ddcb85159e03aeabe59c53722d78a29001"><strong>seqkit/cmd/bed.go</strong></a>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -94,7 +94,7 @@ func ReadBedFilteredFeatures(file string, chrs []string) ([]BedFeature, error) {</td>

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94

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="go">            <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

95

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="go">            <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">*</span><span class="kt" style="color: #458; font-weight: 600;">string</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC96" class="line" lang="go">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">>=</span> <span class="m" style="color: #099;">6</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

97

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<td class="new_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="go">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">items</span><span class="p">[</span><span class="m" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"+"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">items</span><span class="p">[</span><span class="m" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="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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<pre style="margin: 0;">+<span id="LC97" class="line" lang="go">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">items</span><span class="p">[</span><span class="m" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"+"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">items</span><span class="p">[</span><span class="m" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">items</span></span><span class="p"><span class="idiff">[</span></span><span class="m" style="color: #099;"><span class="idiff">5</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"."</span></span><span class="idiff right"> </span><span class="p">{</span></span>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="go">                            <span class="k" style="font-weight: 600;">return</span> <span class="no" style="color: #008080;">nil</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Errorf</span><span class="p">(</span><span class="s" style="color: #d14;">"bad strand: %s"</span><span class="p">,</span> <span class="n" style="color: #333;">items</span><span class="p">[</span><span class="m" style="color: #099;">5</span><span class="p">])</span></span>

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<td class="old_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="go">                    <span class="p">}</span></span>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="go">                   <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">items</span><span class="p">[</span><span class="m" style="color: #099;">5</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -106,7 +106,7 @@ func ReadBedFilteredFeatures(file string, chrs []string) ([]BedFeature, error) {</td>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="go">   <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">!=</span> <span class="no" style="color: #008080;">nil</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="go">           <span class="k" style="font-weight: 600;">return</span> <span class="no" style="color: #008080;">nil</span><span class="p">,</span> <span class="n" style="color: #333;">err</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="go">   <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="go">   <span class="n" style="color: #333;">BedFeatures</span> <span class="o" style="font-weight: 600;">:=</span> <span class="p">[]</span><span class="n" style="color: #333;">BedFeature</span><span class="p"><span class="idiff left right">{}</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="go">   <span class="n" style="color: #333;">BedFeatures</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">make</span></span><span class="p"><span class="idiff">(</span>[]</span><span class="n" style="color: #333;">BedFeature</span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">1024</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="go">   <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">:=</span> <span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Ch</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC111" class="line" lang="go">           <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chunk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Err</span> <span class="o" style="font-weight: 600;">!=</span> <span class="no" style="color: #008080;">nil</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

112

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<td class="new_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(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="LC112" class="line" lang="go">                   <span class="k" style="font-weight: 600;">return</span> <span class="no" style="color: #008080;">nil</span><span class="p">,</span> <span class="n" style="color: #333;">chunk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Err</span></span>

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<li id="1e70a04962951435ea946f5b302ca407674cf304">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#1e70a04962951435ea946f5b302ca407674cf304"><strong>seqkit/cmd/faidx.go</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); 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="264" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -264,7 +264,7 @@ type faidxQuery struct {</td>

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<td class="old_line diff-line-num" data-linenumber="264" style="width: 35px; color: rgba(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="LC264" class="line" lang="go"><span class="k" style="font-weight: 600;">func</span> <span class="n" style="color: #333;">init</span><span class="p">()</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="go">   <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">AddCommand</span><span class="p">(</span><span class="n" style="color: #333;">faidxCmd</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="go">   <span class="n" style="color: #333;">faidxCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"use-regexp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"IDs are regular expression. But subseq region is not suppored here."</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC267" class="line" lang="go">   <span class="n" style="color: #333;">faidxCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"use-regexp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"IDs are regular expression. But subseq region is not suppor<span class="idiff left right">t</span>ed here."</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="go">   <span class="n" style="color: #333;">faidxCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"ignore-case"</span><span class="p">,</span> <span class="s" style="color: #d14;">"i"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"ignore case"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="go">   <span class="n" style="color: #333;">faidxCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"full-head"</span><span class="p">,</span> <span class="s" style="color: #d14;">"f"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"print full header line instead of just ID. New fasta index file ending with .seqkit.fai will be created"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="go">   <span class="n" style="color: #333;">faidxCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">StringP</span><span class="p">(</span><span class="s" style="color: #d14;">"region-file"</span><span class="p">,</span> <span class="s" style="color: #d14;">"l"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"file containing a list of regions"</span><span class="p">)</span></span>

</pre>

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<li id="2bb8272102c7745e0c153fd1d33014c3a7fed384">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#2bb8272102c7745e0c153fd1d33014c3a7fed384"><strong>seqkit/cmd/fq2fa.go</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); 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="41" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -41,7 +41,7 @@ var fq2faCmd = &cobra.Command{</td>

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<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(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="LC41" class="line" lang="go">            <span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">getConfigs</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(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="LC42" class="line" lang="go">            <span class="n" style="color: #333;">alphabet</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Alphabet</span></span>

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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(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="LC43" class="line" lang="go">            <span class="n" style="color: #333;">idRegexp</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">IDRegexp</span></span>

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<td class="old_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="go">            <span class="n" style="color: #333;">lineWidth</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">LineWidth</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC44" class="line" lang="go">            <span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">// </span>lineWidth := config.LineWidth</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(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="LC45" class="line" lang="go">            <span class="n" style="color: #333;">outFile</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OutFile</span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="go">            <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">AlphabetGuessSeqLengthThreshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">AlphabetGuessSeqLength</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="go">            <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ValidateSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">false</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); 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="70" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -70,7 +70,8 @@ var fq2faCmd = &cobra.Command{</td>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="go">                            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="go"></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="go">                            <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="p">{}</span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="go">                            <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">FormatToWriter</span><span class="p">(</span><span class="n" style="color: #333;">outfh</span><span class="p">,</span> <span class="n" style="color: #333;">lineWidth</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="go">                            <span class="c" style="color: #998; font-style: italic;">// record.FormatToWriter(outfh, lineWidth)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC74" class="line" lang="go">                            <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">FormatToWriter</span><span class="p">(</span><span class="n" style="color: #333;">outfh</span><span class="p">,</span> <span class="m" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="go">                    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="go">            <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(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="LC77" class="line" lang="go">    <span class="p">},</span></span>

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<br>

</li>

<li id="76486b4b36e99fed87fd3aeff9124f70d282a3bc">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#76486b4b36e99fed87fd3aeff9124f70d282a3bc"><strong>seqkit/cmd/fx2tab.go</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,7 +26,6 @@ import (</td>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="go">    <span class="s" style="color: #d14;">"encoding/hex"</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="go">    <span class="s" style="color: #d14;">"fmt"</span></span>

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<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(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="LC28" class="line" lang="go">    <span class="s" style="color: #d14;">"io"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="go">    <span class="s" style="color: #d14;">"math"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="go">    <span class="s" style="color: #d14;">"runtime"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="go">    <span class="s" style="color: #d14;">"sort"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="go">    <span class="s" style="color: #d14;">"strings"</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); 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="211" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -212,7 +211,7 @@ Attention:</td>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="go">                           <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="go"></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="go">                           <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">printAvgQual</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="go">                                   <span class="n" style="color: #333;">outfh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WriteString</span><span class="p">(</span><span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Sprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.2f"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">avgQual</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Seq</span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">qBase</span><span class="p">)))</span></span>

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<td class="old_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC214" class="line" lang="go">                                   <span class="n" style="color: #333;">outfh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WriteString</span><span class="p">(</span><span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Sprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.2f"</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Seq</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">AvgQual</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">qBase</span><span class="p">)))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="go">                           <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="go"></span>

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<td class="old_line diff-line-num" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(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="LC217" class="line" lang="go">                           <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">printSeqHash</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -268,16 +267,4 @@ func alphabetStr(s []byte) string {</td>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="go">   <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">strings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Join</span><span class="p">(</span><span class="n" style="color: #333;">alphabet</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="LC268" class="line" lang="go"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="go"></span>

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<td class="old_line diff-line-num old" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC271" class="line" lang="go"><span class="k" style="font-weight: 600;">func</span> <span class="n" style="color: #333;">avgQual</span><span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Seq</span><span class="p">,</span> <span class="n" style="color: #333;">base</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="go">   <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Qual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="m" style="color: #099;">0</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="go">           <span class="k" style="font-weight: 600;">return</span> <span class="m" style="color: #099;">0</span></span>

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<td class="new_line diff-line-num old" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="go">   <span class="p">}</span></span>

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<td class="old_line diff-line-num old" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="go">   <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ParseQual</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="go">   <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">sum</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span></span>

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<td class="old_line diff-line-num old" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="go">   <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">:=</span> <span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">QualValue</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="go">           <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Pow</span><span class="p">(</span><span class="m" style="color: #099;">10</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">)</span><span class="o" style="font-weight: 600;">/-</span><span class="m" style="color: #099;">10</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="go">   <span class="p">}</span></span>

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<td class="old_line diff-line-num old" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="go">   <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Log10</span><span class="p">(</span><span class="n" style="color: #333;">sum</span><span class="o" style="font-weight: 600;">/</span><span class="kt" style="color: #458; font-weight: 600;">float64</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">QualValue</span><span class="p">)))</span></span>

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<pre style="margin: 0;">-<span id="LC281" class="line" lang="go"><span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="go"></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="go"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">_tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="p">{</span><span class="sc" style="color: #d14;">'\t'</span><span class="p">}</span></span></pre>

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<br>

</li>

<li id="a02b528e8138ab6ad3eae788206eb69181c130ba">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#a02b528e8138ab6ad3eae788206eb69181c130ba"><strong>seqkit/cmd/grep.go</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); 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="114" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -114,6 +114,22 @@ Examples:</td>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="go">                   <span class="n" style="color: #333;">checkError</span><span class="p">(</span><span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Errorf</span><span class="p">(</span><span class="s" style="color: #d14;">"one of flags -p (--pattern) and -f (--pattern-file) needed"</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="go">           <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="go">           <span class="c" style="color: #998; font-style: italic;">// check pattern with unquoted comma</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="go">           <span class="n" style="color: #333;">hasUnquotedComma</span> <span class="o" style="font-weight: 600;">:=</span> <span class="no" style="color: #008080;">false</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC119" class="line" lang="go">           <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_pattern</span> <span class="o" style="font-weight: 600;">:=</span> <span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">pattern</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="go">                   <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reUnquotedComma</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MatchString</span><span class="p">(</span><span class="n" style="color: #333;">_pattern</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="go">                           <span class="n" style="color: #333;">hasUnquotedComma</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">true</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

122

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="go">                           <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

123

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="go">                   <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

124

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="go">           <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

125

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="go">           <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hasUnquotedComma</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

126

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="go">                   <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">outFile</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

127

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="go">                           <span class="k" style="font-weight: 600;">defer</span> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Warningf</span><span class="p">(</span><span class="n" style="color: #333;">helpUnquotedComma</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

128

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="go">                   <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

129

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="go">                           <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Warningf</span><span class="p">(</span><span class="n" style="color: #333;">helpUnquotedComma</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

130

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="go">                   <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

131

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="go">           <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

132

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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="LC132" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

117

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<td class="new_line diff-line-num" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

133

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="go">           <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">degenerate</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">bySeq</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

118

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<td class="new_line diff-line-num" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

134

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="go">                   <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"when flag -d (--degenerate) given, flag -s (--by-seq) is automatically on"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

119

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<td class="new_line diff-line-num" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

135

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="go">                   <span class="n" style="color: #333;">bySeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">true</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); 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="659" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -643,3 +659,6 @@ func init() {</td>

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<td class="old_line diff-line-num" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

643

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<td class="new_line diff-line-num" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

659

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC659" class="line" lang="go">   <span class="n" style="color: #333;">grepCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"circular"</span><span class="p">,</span> <span class="s" style="color: #d14;">"c"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"circular genome"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

644

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<td class="new_line diff-line-num" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

660

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC660" class="line" lang="go">   <span class="n" style="color: #333;">grepCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"immediate-output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"I"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"print output immediately, do not use write buffer"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

645

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<td class="new_line diff-line-num" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

661

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC661" class="line" lang="go"><span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

662

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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="LC662" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

663

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="go"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">reUnquotedComma</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">regexp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MustCompile</span><span class="p">(</span><span class="s" style="color: #d14;">`\{[^\}]*$|^[^\{]*\}`</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

664

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<pre style="margin: 0;">+<span id="LC664" class="line" lang="go"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">helpUnquotedComma</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">`possible unquoted comma detected, please use double quotation marks for patterns containing comma, e.g., -p '"A{2,}"' or -p "\"A{2,}\""`</span></span></pre>

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<br>

</li>

<li id="da9f919e44db345f43e899023ccde1e429864c15">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#da9f919e44db345f43e899023ccde1e429864c15"><strong>seqkit/cmd/locate.go</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,6 +103,22 @@ Attentions:</td>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="go">                   <span class="n" style="color: #333;">checkError</span><span class="p">(</span><span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Errorf</span><span class="p">(</span><span class="s" style="color: #d14;">"one of flags -p (--pattern) and -f (--pattern-file) needed"</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="go">           <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC105" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC106" class="line" lang="go">           <span class="c" style="color: #998; font-style: italic;">// check pattern with unquoted comma</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

107

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="go">           <span class="n" style="color: #333;">hasUnquotedComma</span> <span class="o" style="font-weight: 600;">:=</span> <span class="no" style="color: #008080;">false</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC108" class="line" lang="go">           <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_pattern</span> <span class="o" style="font-weight: 600;">:=</span> <span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">pattern</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="go">                   <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reUnquotedComma</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MatchString</span><span class="p">(</span><span class="n" style="color: #333;">_pattern</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

110

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="go">                           <span class="n" style="color: #333;">hasUnquotedComma</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">true</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC111" class="line" lang="go">                           <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC112" class="line" lang="go">                   <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="go">           <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC114" class="line" lang="go">           <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hasUnquotedComma</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="go">                   <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">outFile</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC116" class="line" lang="go">                           <span class="k" style="font-weight: 600;">defer</span> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Warningf</span><span class="p">(</span><span class="n" style="color: #333;">helpUnquotedComma</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="go">                   <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

118

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="go">                           <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Warningf</span><span class="p">(</span><span class="n" style="color: #333;">helpUnquotedComma</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

119

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="go">                   <span class="p">}</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

120

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="go">           <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

121

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

122

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="go">           <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mismatches</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

123

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC123" class="line" lang="go">                   <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">degenerate</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

124

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="go">                           <span class="n" style="color: #333;">checkError</span><span class="p">(</span><span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Errorf</span><span class="p">(</span><span class="s" style="color: #d14;">"flag -d (--degenerate) not allowed when giving flag -m (--max-mismatch)"</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -906,6 +922,7 @@ Attentions:</td>

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<td class="old_line diff-line-num" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

906

</td>

<td class="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC922" class="line" lang="go">                           <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

907

</td>

<td class="new_line diff-line-num" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

923

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC923" class="line" lang="go">                   <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

908

</td>

<td class="new_line diff-line-num" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

924

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<pre style="margin: 0;"> <span id="LC924" class="line" lang="go">           <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

925

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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="LC925" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num" 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

</td>

<td class="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC926" class="line" lang="go">   <span class="p">},</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC927" class="line" lang="go"><span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC928" class="line" lang="go"></span>

</pre>

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<br>

</li>

<li id="29fe4b7c1fedb5f9aec18990085490fee6564b10">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#29fe4b7c1fedb5f9aec18990085490fee6564b10"><strong>seqkit/cmd/mutate.go</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); 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="43" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -43,7 +43,7 @@ var mutateCmd = &cobra.Command{</td>

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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC43" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC44" class="line" lang="go"><span class="s" style="color: #d14;">Attentions:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC45" class="line" lang="go"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

46

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<td class="new_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="go"><span class="s" style="color: #d14;">  1. Mutiple point mutations (-p/--point) are allowed, but only single<span class="idiff left right"> </span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC46" class="line" lang="go"><span class="s" style="color: #d14;">  1. Mu<span class="idiff left right">l</span>tiple point mutations (-p/--point) are allowed, but only single</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="go"><span class="s" style="color: #d14;">     insertion (-i/--insertion) OR single deletion (-d/--deletion) is allowed.</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="go"><span class="s" style="color: #d14;">  2. Point mutation takes place before insertion/deletion.</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="go"></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">@@ -135,6 +135,22 @@ Examples:</td>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="go">           <span class="c" style="color: #998; font-style: italic;">//   checkError(fmt.Errorf("one of flags -p (--pattern) and -f (--pattern-file) needed"))</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="go">           <span class="c" style="color: #998; font-style: italic;">// }</span></span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="go"></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="go">           <span class="c" style="color: #998; font-style: italic;">// check pattern with unquoted comma</span></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="go">           <span class="n" style="color: #333;">hasUnquotedComma</span> <span class="o" style="font-weight: 600;">:=</span> <span class="no" style="color: #008080;">false</span></span>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="go">           <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_pattern</span> <span class="o" style="font-weight: 600;">:=</span> <span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">pattern</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="go">                   <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reUnquotedComma</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MatchString</span><span class="p">(</span><span class="n" style="color: #333;">_pattern</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="go">                           <span class="n" style="color: #333;">hasUnquotedComma</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">true</span></span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="go">                           <span class="k" style="font-weight: 600;">break</span></span>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="go">                   <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="go">           <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="go">           <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hasUnquotedComma</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="go">                   <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">outFile</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="go">                           <span class="k" style="font-weight: 600;">defer</span> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Warningf</span><span class="p">(</span><span class="n" style="color: #333;">helpUnquotedComma</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="go">                   <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC150" class="line" lang="go">                           <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Warningf</span><span class="p">(</span><span class="n" style="color: #333;">helpUnquotedComma</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

151

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="go">                   <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC152" class="line" lang="go">           <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

153

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

138

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<td class="new_line diff-line-num" data-linenumber="154" style="width: 35px; color: rgba(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="LC154" class="line" lang="go">           <span class="c" style="color: #998; font-style: italic;">// prepare pattern</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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<td class="new_line diff-line-num" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

155

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="go">           <span class="n" style="color: #333;">patterns</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nb" style="color: #0086b3;">make</span><span class="p">(</span><span class="k" style="font-weight: 600;">map</span><span class="p">[</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">regexp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Regexp</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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<td class="new_line diff-line-num" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

156

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="go">           <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">patternFile</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span> <span class="p">{</span></span>

</pre>

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<br>

</li>

<li id="604fd55a896e470ee80f4ea9caf71f879579d68c">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#604fd55a896e470ee80f4ea9caf71f879579d68c"><strong>seqkit/cmd/pair.go</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); 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="65" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -65,7 +65,7 @@ Attensions:</td>

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<td class="old_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<td class="new_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="go">            <span class="n" style="color: #333;">runtime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GOMAXPROCS</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Threads</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

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<td class="new_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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<td class="new_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(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="LC67" class="line" lang="go">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

68

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<td class="new_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="go">                    <span class="n" style="color: #333;">checkError</span><span class="p">(</span><span class="n" style="color: #333;">errors</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">New</span><span class="p">(</span><span class="s" style="color: #d14;">"no positional ar<span class="idiff left right">u</span>gments are allowed"</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

68

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="go">                    <span class="n" style="color: #333;">checkError</span><span class="p">(</span><span class="n" style="color: #333;">errors</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">New</span><span class="p">(</span><span class="s" style="color: #d14;">"no positional arg<span class="idiff left right">u</span>ments are allowed"</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

69

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<td class="new_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

69

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="go">            <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

70

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<td class="new_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

70

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

71

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<td class="new_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

71

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="go">            <span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">getFlagString</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="s" style="color: #d14;">"read1"</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="32f77b9b26ba8c525e818703d5ae667b751cebef">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#32f77b9b26ba8c525e818703d5ae667b751cebef"><strong>seqkit/cmd/replace.go</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); 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="241" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -241,7 +241,7 @@ func init() {</td>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="go">                   <span class="s" style="color: #d14;">"ATTENTION: for *nix OS, use SINGLE quote NOT double quotes or "</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="go">                   <span class="s" style="color: #d14;">`use the \ escape character. Record number is also supported by "{nr}".`</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="go">                   <span class="s" style="color: #d14;">`use ${1} instead of $1 when {kv} given!`</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="go">   <span class="n" style="color: #333;">replaceCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">IntP</span><span class="p">(</span><span class="s" style="color: #d14;">"nr-width"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">`minimum width for {nr} in flag -r/--replacement. e.g., formating "1" to "001" by --nr-width 3`</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC244" class="line" lang="go">   <span class="n" style="color: #333;">replaceCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">IntP</span><span class="p">(</span><span class="s" style="color: #d14;">"nr-width"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">`minimum width for {nr} in flag -r/--replacement. e.g., format<span class="idiff left right">t</span>ing "1" to "001" by --nr-width 3`</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="go">   <span class="c" style="color: #998; font-style: italic;">// replaceCmd.Flags().BoolP("by-name", "n", false, "replace full name instead of just id")</span></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="go">   <span class="n" style="color: #333;">replaceCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"by-seq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"s"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"replace seq (only FASTA)"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="go">   <span class="n" style="color: #333;">replaceCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"ignore-case"</span><span class="p">,</span> <span class="s" style="color: #d14;">"i"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"ignore case"</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="fb73906bdb791ca7cb1138a6de00ba5ad4521465">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#fb73906bdb791ca7cb1138a6de00ba5ad4521465"><strong>seqkit/cmd/root.go</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); 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="82" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -82,11 +82,14 @@ func init() {</td>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="go">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="go">    <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PersistentFlags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">StringP</span><span class="p">(</span><span class="s" style="color: #d14;">"seq-type"</span><span class="p">,</span> <span class="s" style="color: #d14;">"t"</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto"</span><span class="p">,</span> <span class="s" style="color: #d14;">"sequence type (dna|rna|protein|unlimit|auto) (for auto, it automatically detect by the first sequence)"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="84" style="width: 35px; color: rgba(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="LC84" class="line" lang="go">    <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PersistentFlags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">IntP</span><span class="p">(</span><span class="s" style="color: #d14;">"threads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"j"</span><span class="p">,</span> <span class="n" style="color: #333;">defaultThreads</span><span class="p">,</span> <span class="s" style="color: #d14;">"number of CPUs. can also set with environment variable SEQKIT_THREADS)"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="go">    <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PersistentFlags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">IntP</span><span class="p">(</span><span class="s" style="color: #d14;">"line-width"</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">,</span> <span class="m" style="color: #099;">60</span><span class="p">,</span> <span class="s" style="color: #d14;">"line width when outputing FASTA format (0 for no wrap)"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC85" class="line" lang="go">    <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PersistentFlags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">IntP</span><span class="p">(</span><span class="s" style="color: #d14;">"line-width"</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">,</span> <span class="m" style="color: #099;">60</span><span class="p">,</span> <span class="s" style="color: #d14;">"line width when output<span class="idiff left right">t</span>ing FASTA format (0 for no wrap)"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="go">    <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PersistentFlags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">StringP</span><span class="p">(</span><span class="s" style="color: #d14;">"id-regexp"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">fastx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DefaultIDRegexp</span><span class="p">,</span> <span class="s" style="color: #d14;">"regular expression for parsing ID"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="go">    <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PersistentFlags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"id-ncbi"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"FASTA head is NCBI-style, e.g. >gi|110645304|ref|NC_002516.2| Pseud..."</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC88" class="line" lang="go">    <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PersistentFlags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">StringP</span><span class="p">(</span><span class="s" style="color: #d14;">"out-file"</span><span class="p">,</span> <span class="s" style="color: #d14;">"o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span> <span class="s" style="color: #d14;">`out file ("-" for stdout, suffix .gz for gzipped out)`</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

</td>

<td class="new_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="go">    <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PersistentFlags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"quiet"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"be quiet and do not show extra information"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

90

</td>

<td class="new_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

90

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="go">    <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PersistentFlags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">IntP</span><span class="p">(</span><span class="s" style="color: #d14;">"alphabet-guess-seq-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="m" style="color: #099;">10000</span><span class="p">,</span> <span class="s" style="color: #d14;">"length of sequence prefix of the first FASTA record based on which seqkit guesses the sequence type (0 for whole seq)"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC91" class="line" lang="go">    <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PersistentFlags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">StringP</span><span class="p">(</span><span class="s" style="color: #d14;">"infile-list"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"file of input files list (one file per line), if given, they are appended to files from cli arguments"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

92

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC92" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

93

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="go">    <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">CompletionOptions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DisableDefaultCmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">true</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

94

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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="LC94" class="line" lang="go">    <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SetHelpCommand</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cobra</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Command</span><span class="p">{</span><span class="n" style="color: #333;">Hidden</span><span class="o" style="font-weight: 600;">:</span> <span class="no" style="color: #008080;">true</span><span class="p">})</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

95

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC95" class="line" lang="go"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="f6639935f1c63a101930babdf188dc5db8749963">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#f6639935f1c63a101930babdf188dc5db8749963"><strong>seqkit/cmd/scat.go</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -566,7 +566,7 @@ func init() {</td>

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<td class="old_line diff-line-num" 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">

566

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<td class="new_line diff-line-num" 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">

566

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<pre style="margin: 0;"> <span id="LC566" class="line" lang="go">   <span class="n" style="color: #333;">scatCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">StringP</span><span class="p">(</span><span class="s" style="color: #d14;">"in-format"</span><span class="p">,</span> <span class="s" style="color: #d14;">"I"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"input format: fastq or fasta (fastq)"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

567

</td>

<td class="new_line diff-line-num" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

567

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC567" class="line" lang="go">   <span class="n" style="color: #333;">scatCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">StringP</span><span class="p">(</span><span class="s" style="color: #d14;">"out-format"</span><span class="p">,</span> <span class="s" style="color: #d14;">"O"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"output format: fastq or fasta"</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

568

</td>

<td class="new_line diff-line-num" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

568

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC568" class="line" lang="go">   <span class="n" style="color: #333;">scatCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"allow-gaps"</span><span class="p">,</span> <span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"allow gap character (-) in sequences"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

569

</td>

<td class="new_line diff-line-num old" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC569" class="line" lang="go">   <span class="n" style="color: #333;">scatCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"find-only"</span><span class="p">,</span> <span class="s" style="color: #d14;">"f"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"concatenate exis<span class="idiff left right">i</span>ting files and quit"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

569

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<pre style="margin: 0;">+<span id="LC569" class="line" lang="go">   <span class="n" style="color: #333;">scatCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"find-only"</span><span class="p">,</span> <span class="s" style="color: #d14;">"f"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"concatenate existing files and quit"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC570" class="line" lang="go">   <span class="n" style="color: #333;">scatCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"gz-only"</span><span class="p">,</span> <span class="s" style="color: #d14;">"g"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"only look for gzipped files (.gz suffix)"</span><span class="p">)</span></span>

</pre>

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571

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<td class="new_line diff-line-num" data-linenumber="571" style="width: 35px; color: rgba(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="LC571" class="line" lang="go">   <span class="n" style="color: #333;">scatCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">StringP</span><span class="p">(</span><span class="s" style="color: #d14;">"time-limit"</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"quit after inactive for this time period"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC572" class="line" lang="go">   <span class="n" style="color: #333;">scatCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">IntP</span><span class="p">(</span><span class="s" style="color: #d14;">"wait-pid"</span><span class="p">,</span> <span class="s" style="color: #d14;">"p"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"after process with this PID exited"</span><span class="p">)</span></span>

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<br>

</li>

<li id="1d415668e438829ee466a5e6b51f9c42ca064b0c">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#1d415668e438829ee466a5e6b51f9c42ca064b0c"><strong>seqkit/cmd/shuffle.go</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -46,7 +46,7 @@ For FASTA format, use flag -2 (--two-pass) to reduce memory usage. FASTQ not</td>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="go"><span class="s" style="color: #d14;">supported.</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="go"></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="go"><span class="s" style="color: #d14;">Firstly, seqkit reads the sequence IDs. If the file is not plain FASTA file,</span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="go"><span class="s" style="color: #d14;">seqkit will write the sequences to tempory files, and create FASTA index.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="go"><span class="s" style="color: #d14;">seqkit will write the sequences to tempor<span class="idiff left right">ar</span>y files, and create FASTA index.</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="go"></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="go"><span class="s" style="color: #d14;">Secondly, seqkit shuffles sequence IDs and extract sequences by FASTA index.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="go"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); 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="149" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -149,7 +149,7 @@ Secondly, seqkit shuffles sequence IDs and extract sequences by FASTA index.</td>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="go">                           <span class="n" style="color: #333;">newFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fastx"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="go">                   <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="go">                   <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">quiet</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="go">                           <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"read and write sequences to tempory file: %s ..."</span><span class="p">,</span> <span class="n" style="color: #333;">newFile</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="go">                           <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"read and write sequences to tempor<span class="idiff left right">ar</span>y file: %s ..."</span><span class="p">,</span> <span class="n" style="color: #333;">newFile</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="go">                   <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="go"></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="go">                   <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">nseqs</span> <span class="kt" style="color: #458; font-weight: 600;">int</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">@@ -233,5 +233,5 @@ func init() {</td>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="go">   <span class="n" style="color: #333;">RootCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">AddCommand</span><span class="p">(</span><span class="n" style="color: #333;">shuffleCmd</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="go">   <span class="n" style="color: #333;">shuffleCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Int64P</span><span class="p">(</span><span class="s" style="color: #d14;">"rand-seed"</span><span class="p">,</span> <span class="s" style="color: #d14;">"s"</span><span class="p">,</span> <span class="m" style="color: #099;">23</span><span class="p">,</span> <span class="s" style="color: #d14;">"rand seed for shuffle"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="go">   <span class="n" style="color: #333;">shuffleCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"two-pass"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"two-pass mode read files twice to lower memory usage. (only for FASTA format)"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="go">   <span class="n" style="color: #333;">shuffleCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"keep-temp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"k"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"keep tempory FASTA and .fai file when using 2-pass mode"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC236" class="line" lang="go">   <span class="n" style="color: #333;">shuffleCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"keep-temp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"k"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"keep tempor<span class="idiff left right">ar</span>y FASTA and .fai file when using 2-pass mode"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="go"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="92b5b49951aa33ccf0a6d8b10622240cc64511e8">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#92b5b49951aa33ccf0a6d8b10622240cc64511e8"><strong>seqkit/cmd/sort.go</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="go"></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="go"><span class="s" style="color: #d14;">Firstly, seqkit reads the sequence head and length information.</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="go"><span class="s" style="color: #d14;">If the file is not plain FASTA file,</span></span>

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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="go"><span class="s" style="color: #d14;">seqkit will write the sequences to tempory files, and create FASTA index.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="go"><span class="s" style="color: #d14;">seqkit will write the sequences to tempor<span class="idiff left right">ar</span>y files, and create FASTA index.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="go"></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="go"><span class="s" style="color: #d14;">Secondly, seqkit sorts sequence by head and length information</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="go"><span class="s" style="color: #d14;">and extracts sequences by FASTA index.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); 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="255" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -255,7 +255,7 @@ and extracts sequences by FASTA index.</td>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="go">                           <span class="n" style="color: #333;">newFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fastx"</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="go">                   <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="go">                   <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">quiet</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC258" class="line" lang="go">                           <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"read and write sequences to tempory file: %s ..."</span><span class="p">,</span> <span class="n" style="color: #333;">newFile</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="go">                           <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"read and write sequences to tempor<span class="idiff left right">ar</span>y file: %s ..."</span><span class="p">,</span> <span class="n" style="color: #333;">newFile</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="go">                   <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="go"></span>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="go">                   <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">nseqs</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -463,6 +463,6 @@ func init() {</td>

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<pre style="margin: 0;"> <span id="LC463" class="line" lang="go">   <span class="n" style="color: #333;">sortCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"ignore-case"</span><span class="p">,</span> <span class="s" style="color: #d14;">"i"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"ignore case"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="go"></span>

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="go">   <span class="n" style="color: #333;">sortCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"two-pass"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"two-pass mode read files twice to lower memory usage. (only for FASTA format)"</span><span class="p">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC466" class="line" lang="go">   <span class="n" style="color: #333;">sortCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"keep-temp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"k"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"keep tempory FASTA and .fai file when using 2-pass mode"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="go">   <span class="n" style="color: #333;">sortCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"keep-temp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"k"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"keep tempor<span class="idiff left right">ar</span>y FASTA and .fai file when using 2-pass mode"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC467" class="line" lang="go">   <span class="n" style="color: #333;">sortCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">IntP</span><span class="p">(</span><span class="s" style="color: #d14;">"seq-prefix-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"L"</span><span class="p">,</span> <span class="m" style="color: #099;">10000</span><span class="p">,</span> <span class="s" style="color: #d14;">"length of sequence prefix on which seqkit sorts by sequences (0 for whole sequence)"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="468" style="width: 35px; color: rgba(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="LC468" class="line" lang="go"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="ecd9ca523ede3e6b5b35186b55d0ce7e3198e7c9">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#ecd9ca523ede3e6b5b35186b55d0ce7e3198e7c9"><strong>seqkit/cmd/split.go</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); 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="196" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -196,7 +196,7 @@ Examples:</td>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="go">                                   <span class="n" style="color: #333;">newFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fastx"</span></span>

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<td class="old_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(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="LC197" class="line" lang="go">                           <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(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="LC198" class="line" lang="go">                           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">quiet</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="go">                                   <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"read and write sequences to tempory file: %s ..."</span><span class="p">,</span> <span class="n" style="color: #333;">newFile</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC199" class="line" lang="go">                                   <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"read and write sequences to tempor<span class="idiff left right">ar</span>y file: %s ..."</span><span class="p">,</span> <span class="n" style="color: #333;">newFile</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(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="LC200" class="line" lang="go">                           <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(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="LC201" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(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="LC202" class="line" lang="go">                           <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">nseqs</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); 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="362" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -362,7 +362,7 @@ Examples:</td>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="go">                                   <span class="n" style="color: #333;">newFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fastx"</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="363" style="width: 35px; color: rgba(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="LC363" class="line" lang="go">                           <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="364" style="width: 35px; color: rgba(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="LC364" class="line" lang="go">                           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">quiet</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num old" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="go">                                   <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"read and write sequences to tempory file: %s ..."</span><span class="p">,</span> <span class="n" style="color: #333;">newFile</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC365" class="line" lang="go">                                   <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"read and write sequences to tempor<span class="idiff left right">ar</span>y file: %s ..."</span><span class="p">,</span> <span class="n" style="color: #333;">newFile</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="366" style="width: 35px; color: rgba(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="LC366" class="line" lang="go">                           <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="367" style="width: 35px; color: rgba(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="LC367" class="line" lang="go"></span>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="go">                           <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">nseqs</span> <span class="kt" style="color: #458; font-weight: 600;">int</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">@@ -458,11 +458,17 @@ Examples:</td>

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<pre style="margin: 0;"> <span id="LC458" class="line" lang="go">                                   <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="m" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="go">                           <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC460" class="line" lang="go">                   <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC461" class="line" lang="go">                   <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">quiet</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC462" class="line" lang="go">                           <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"write %d sequences to file: %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;">j</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC463" class="line" lang="go">                   <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC464" class="line" lang="go">                   <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">dryRun</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC465" class="line" lang="go">                           <span class="n" style="color: #333;">outfh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Close</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC461" class="line" lang="go">                   <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="go">                           <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">quiet</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC463" class="line" lang="go">                                   <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"write %d sequences to file: %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;">j</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC464" class="line" lang="go">                           <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC465" class="line" lang="go">                           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">dryRun</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="go">                                   <span class="n" style="color: #333;">outfh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Close</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="go">                           <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC468" class="line" lang="go">                   <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC469" class="line" lang="go">                           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">dryRun</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

470

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<pre style="margin: 0;">+<span id="LC470" class="line" lang="go">                                   <span class="n" style="color: #333;">checkError</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Remove</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

471

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<pre style="margin: 0;">+<span id="LC471" class="line" lang="go">                           <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

466

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<td class="new_line diff-line-num" data-linenumber="472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

472

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="go">                   <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

467

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<td class="new_line diff-line-num" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

473

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

468

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<td class="new_line diff-line-num" data-linenumber="474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

474

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="go">                   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isstdin</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isPlainFile</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">keepTemp</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -531,7 +537,7 @@ Examples:</td>

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<td class="old_line diff-line-num" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

531

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<td class="new_line diff-line-num" 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="go">                                   <span class="n" style="color: #333;">newFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fastx"</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="go">                           <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

539

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC539" class="line" lang="go">                           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">quiet</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

534

</td>

<td class="new_line diff-line-num old" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC534" class="line" lang="go">                                   <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"read and write sequences to tempory file: %s ..."</span><span class="p">,</span> <span class="n" style="color: #333;">newFile</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

540

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<pre style="margin: 0;">+<span id="LC540" class="line" lang="go">                                   <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"read and write sequences to tempor<span class="idiff left right">ar</span>y file: %s ..."</span><span class="p">,</span> <span class="n" style="color: #333;">newFile</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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">

541

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="go">                           <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

536

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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC542" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

543

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC543" class="line" lang="go">                           <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">nseqs</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); 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="561" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -555,7 +561,7 @@ Examples:</td>

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<td class="old_line diff-line-num" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

555

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<td class="new_line diff-line-num" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

561

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<pre style="margin: 0;"> <span id="LC561" class="line" lang="go">                           <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

556

</td>

<td class="new_line diff-line-num" 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">

562

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<pre style="margin: 0;"> <span id="LC562" class="line" lang="go">                           <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isFastq</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

557

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<td class="new_line diff-line-num" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

563

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<pre style="margin: 0;"> <span id="LC563" class="line" lang="go">                                   <span class="n" style="color: #333;">checkError</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Remove</span><span class="p">(</span><span class="n" style="color: #333;">newFile</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

558

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<td class="new_line diff-line-num old" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC558" class="line" lang="go">                                   <span class="n" style="color: #333;">checkError</span><span class="p">(</span><span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Errorf</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">S</span>orry, two-pass mode does not support FASTQ format"</span><span class="p">))</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

564

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<pre style="margin: 0;">+<span id="LC564" class="line" lang="go">                                   <span class="n" style="color: #333;">checkError</span><span class="p">(</span><span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Errorf</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">s</span>orry, two-pass mode does not support FASTQ format"</span><span class="p">))</span></span>

</pre>

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559

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<td class="new_line diff-line-num" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

565

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<pre style="margin: 0;"> <span id="LC565" class="line" lang="go">                           <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

560

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566

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<pre style="margin: 0;"> <span id="LC566" class="line" lang="go">                   <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

561

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<td class="new_line diff-line-num" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

567

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<pre style="margin: 0;"> <span id="LC567" class="line" lang="go">                   <span class="n" style="color: #333;">fileExt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">suffixFA</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); 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="728" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -722,7 +728,7 @@ Examples:</td>

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<td class="old_line diff-line-num" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

722

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<td class="new_line diff-line-num" data-linenumber="728" style="width: 35px; color: rgba(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="LC728" class="line" lang="go">                                   <span class="n" style="color: #333;">newFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fastx"</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="729" style="width: 35px; color: rgba(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="LC729" class="line" lang="go">                           <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

724

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<td class="new_line diff-line-num" data-linenumber="730" style="width: 35px; color: rgba(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="LC730" class="line" lang="go">                           <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">quiet</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

725

</td>

<td class="new_line diff-line-num old" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC725" class="line" lang="go">                                   <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"read and write sequences to tempory file: %s ..."</span><span class="p">,</span> <span class="n" style="color: #333;">newFile</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

731

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<pre style="margin: 0;">+<span id="LC731" class="line" lang="go">                                   <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Infof</span><span class="p">(</span><span class="s" style="color: #d14;">"read and write sequences to tempor<span class="idiff left right">ar</span>y file: %s ..."</span><span class="p">,</span> <span class="n" style="color: #333;">newFile</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

726

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<td class="new_line diff-line-num" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

732

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<pre style="margin: 0;"> <span id="LC732" class="line" lang="go">                           <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

727

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<td class="new_line diff-line-num" 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">

733

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<pre style="margin: 0;"> <span id="LC733" class="line" lang="go"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

728

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<td class="new_line diff-line-num" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

734

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<pre style="margin: 0;"> <span id="LC734" class="line" lang="go">                           <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">nseqs</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -854,7 +860,7 @@ func init() {</td>

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854

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC860" class="line" lang="go">           <span class="s" style="color: #d14;">`e.g 1:12 for first 12 bases, -12:-1 for last 12 bases. type "seqkit split -h" for more examples`</span><span class="p">)</span></span>

</pre>

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855

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<td class="new_line diff-line-num" 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="go">   <span class="n" style="color: #333;">splitCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"two-pass"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"two-pass mode read files twice to lower memory usage. (only for FASTA format)"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

856

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<td class="new_line diff-line-num" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

862

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<pre style="margin: 0;"> <span id="LC862" class="line" lang="go">   <span class="n" style="color: #333;">splitCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"dry-run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"d"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"dry run, just print message and no files will be created."</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

857

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<td class="new_line diff-line-num old" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC857" class="line" lang="go">   <span class="n" style="color: #333;">splitCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"keep-temp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"k"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"keep tempory FASTA and .fai file when using 2-pass mode"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

863

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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="LC863" class="line" lang="go">   <span class="n" style="color: #333;">splitCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"keep-temp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"k"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"keep tempor<span class="idiff left right">ar</span>y FASTA and .fai file when using 2-pass mode"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" 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

</td>

<td class="new_line diff-line-num" 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="go">   <span class="n" style="color: #333;">splitCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">StringP</span><span class="p">(</span><span class="s" style="color: #d14;">"out-dir"</span><span class="p">,</span> <span class="s" style="color: #d14;">"O"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"output directory (default value is $infile.split)"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC865" class="line" lang="go">   <span class="n" style="color: #333;">splitCmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Flags</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BoolP</span><span class="p">(</span><span class="s" style="color: #d14;">"force"</span><span class="p">,</span> <span class="s" style="color: #d14;">"f"</span><span class="p">,</span> <span class="no" style="color: #008080;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"overwrite output directory"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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">

866

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC866" class="line" lang="go"><span class="p">}</span></span>

</pre>

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</li>

<li id="08f4007a2dcdd77b75167cfe678d33d187bd0572">

<a href="https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4#08f4007a2dcdd77b75167cfe678d33d187bd0572"><strong>tests/test.sh</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); 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="203" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -203,7 +203,7 @@ assert_equal $(cat $STDOUT_FILE | md5sum | cut -d" " -f 1) $($app seq $file | md</td>

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203

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<td class="new_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

203

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="shell"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

204

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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

204

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="shell"><span class="nv" style="color: #008080;">file</span><span class="o" style="font-weight: 600;">=</span>tests/reads_1.fq.gz</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

205

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<td class="new_line diff-line-num" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

205

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="shell">run fq2fa <span class="nv" style="color: #008080;">$app</span> fq2fa <span class="nv" style="color: #008080;">$file</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

206

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<td class="new_line diff-line-num old" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="shell">assert_equal <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$STDOUT_FILE</span> | <span class="nb" style="color: #0086b3;">md5sum</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span><span class="s2" style="color: #d14;">" "</span> <span class="nt" style="color: #000080;">-f</span> 1<span class="si" style="color: #d14;">)</span> <span class="si" style="color: #d14;">$(</span><span class="nv" style="color: #008080;">$app</span> fx2tab <span class="nv" style="color: #008080;">$file</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f</span> 1,2 | <span class="nv" style="color: #008080;">$app</span> tab2fx | <span class="nb" style="color: #0086b3;">md5sum</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span><span class="s2" style="color: #d14;">" "</span> <span class="nt" style="color: #000080;">-f</span> 1<span class="si" style="color: #d14;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

206

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="shell">assert_equal <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$STDOUT_FILE</span> | <span class="nb" style="color: #0086b3;">md5sum</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span><span class="s2" style="color: #d14;">" "</span> <span class="nt" style="color: #000080;">-f</span> 1<span class="si" style="color: #d14;">)</span> <span class="si" style="color: #d14;">$(</span><span class="nv" style="color: #008080;">$app</span> fx2tab <span class="nv" style="color: #008080;">$file</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f</span> 1,2 | <span class="nv" style="color: #008080;">$app</span> tab2fx <span class="nt" style="color: #000080;"><span class="idiff left">-w</span></span><span class="idiff right"> 0 </span>| <span class="nb" style="color: #0086b3;">md5sum</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span><span class="s2" style="color: #d14;">" "</span> <span class="nt" style="color: #000080;">-f</span> 1<span class="si" style="color: #d14;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

207

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<td class="new_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

207

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC207" class="line" lang="shell"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

208

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<td class="new_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

208

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="shell"><span class="nv" style="color: #008080;">READS_FQ</span><span class="o" style="font-weight: 600;">=</span>tests/pcs109_5k.fq</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

209

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<td class="new_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

209

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="shell"><span class="nv" style="color: #008080;">NANO_FQ_TSV</span><span class="o" style="font-weight: 600;">=</span>tests/pcs109_5k_fq_NanoPlot.tsv</span>

</pre>

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