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<h3>
Nilesh Patra pushed to branch master
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/fdab9ef8bbaef45f60d4b7f06a40b22e0039b24d">fdab9ef8</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-03T18:29:56+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.12.1+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/1173ccfbfd07f401e4d2b8b23763752295c2f638">1173ccfb</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-03T18:30:28+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.12.1+ds'
Update to upstream version '0.12.1+ds'
with Debian dir 6ed0ab594a77ea01f4ab7064d95730af53b73c85</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/a51b6bed7ce08f0d58f978ecbf755bd8c46c67d3">a51b6bed</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-03T18:31:16+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Repack to remove generated files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/e6e87bf3104fd1a0ad3d647616a8438767fa33d1">e6e87bf3</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-03T19:17:15+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/2c2feb26d8ef4fcd2a031b0000a55afe731027d6">2c2feb26</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-03T19:27:23+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spellings
</pre>
</li>
</ul>
<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec0b0823b92126645d453bd4242b0ad874ac054">
<span class="deleted-file">
−
benchmark/revcom_biogo
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
</span>
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</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#550668b2fd920123de6e240cb6e63ceaa5c53dc3">
<span class="new-file">
+
debian/patches/spellings.patch
</span>
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<li class="file-stats">
<a href="#589b0da1474d6fcebfbeb88b464ffa5e9d91a132">
<span class="new-file">
+
debian/seqkit-benchmark.1
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<li class="file-stats">
<a href="#936f94415260b98c932db319f298c89c1cd7a783">
<span class="new-file">
+
debian/seqkit.1
</span>
</a>
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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<li class="file-stats">
<a href="#a14f3e9f63bfcdc0edae53df40500f79a4d10c6b">
<span class="deleted-file">
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tests/pcs109_5k.bam
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<li class="file-stats">
<a href="#e4e6de67e4bb4c6122d021ab02cae8891dfdfa0d">
<span class="deleted-file">
−
tests/pcs109_5k.bam.bai
</span>
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<a href="#c13ad171ce2c2d2f5b1efc0f554dcd673fd11158">
<span class="deleted-file">
−
tests/pcs109_5k_prim.bam
</span>
</a>
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<li class="file-stats">
<a href="#de576c405abafa8a6db072c7f5f292b3e9710034">
<span class="deleted-file">
−
tests/pcs109_5k_prim.bam.bai
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</a>
</li>
<li class="file-stats">
<a href="#46a230a5573fc66b721acc0676df40509f0a7b18">
<span class="deleted-file">
−
tests/pcs109_5k_spliced.bam
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</a>
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<li class="file-stats">
<a href="#ad38a0d04389bc1cac7330b44fdd735b267ccf96">
<span class="deleted-file">
−
tests/pcs109_5k_spliced.bam.bai
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="8ec0b0823b92126645d453bd4242b0ad874ac054">
<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#8ec0b0823b92126645d453bd4242b0ad874ac054"><strong>benchmark/revcom_biogo</strong>
deleted
</a>
<hr>
No preview for this file type
<br>
</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">seqkit (0.12.1-1) UNRELEASED; urgency=medium</span>
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<td class="diff-line-num new new_line" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">seqkit (0.12.1<span class="idiff left right">+ds</span>-1) UNRELEASED; urgency=medium</span>
</pre>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<bug>)</span>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> TODO: https://salsa.debian.org/go-team/packages/golang-github-biogo-biogo</span>
</pre>
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</li>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
</pre>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: SeqKit</span>
</pre>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: https://github.com/shenwei356/seqkit/releases</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Files-Excluded: benchmark/revcom_biogo</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> tests/*.bam*</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Files: *</span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Copyright: 2016-2020 Wei Shen, 2019 Oxford Nanopore Technologies.</span>
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<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>seqkit</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-h"</span> <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>seqkit-benchmark</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use-upstream-go-logger.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">spellings.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#550668b2fd920123de6e240cb6e63ceaa5c53dc3"><strong>debian/patches/spellings.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Nilesh Patra <npatra974@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Fix spellings in the package</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last Changed: August 3, 2020</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/seqkit/cmd/bam.go</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/seqkit/cmd/bam.go</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -754,14 +754,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> fmap["RefAln"] = fieldInfo{</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "Aligned refence length",</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "Aligned reference length",</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> func(r *sam.Record) float64 {</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> return float64(r.Len())</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> },</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> fmap["RefCov"] = fieldInfo{</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "Refence coverage",</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "Reference coverage",</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> func(r *sam.Record) float64 {</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> return float64(r.Len()) / float64(r.Ref.Len()) * 100</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> },</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/seqkit/cmd/faidx.go</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/seqkit/cmd/faidx.go</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -205,7 +205,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> func init() {</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> RootCmd.AddCommand(faidxCmd)</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- faidxCmd.Flags().BoolP("use-regexp", "r", false, "IDs are regular expression. But subseq region is not suppored here.")</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ faidxCmd.Flags().BoolP("use-regexp", "r", false, "IDs are regular expression. But subseq region is not supported here.")</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> faidxCmd.Flags().BoolP("ignore-case", "i", false, "ignore case")</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> faidxCmd.Flags().BoolP("full-head", "f", false, "print full header line instead of just ID. New fasta index file ending with .seqkit.fai will be created")</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/seqkit/cmd/mutate.go</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/seqkit/cmd/mutate.go</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -43,7 +43,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> Attentions:</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 1. Mutiple point mutations (-p/--point) are allowed, but only single </span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 1. Multiple point mutations (-p/--point) are allowed, but only single </span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> insertion (-i/--insertion) OR single deletion (-d/--deletion) is allowed.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> 2. Point mutation takes place before insertion/deletion.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/seqkit/cmd/replace.go</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/seqkit/cmd/replace.go</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="p">@@ -220,7 +220,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> "ATTENTION: for *nix OS, use SINGLE quote NOT double quotes or "+</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> `use the \ escape character. Record number is also supported by "{nr}".`+</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> `use ${1} instead of $1 when {kv} given!`)</span>
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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- replaceCmd.Flags().IntP("nr-width", "", 1, `minimum width for {nr} in flag -r/--replacement. e.g., formating "1" to "001" by --nr-width 3`)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ replaceCmd.Flags().IntP("nr-width", "", 1, `minimum width for {nr} in flag -r/--replacement. e.g., formatting "1" to "001" by --nr-width 3`)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> // replaceCmd.Flags().BoolP("by-name", "n", false, "replace full name instead of just id")</span>
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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> replaceCmd.Flags().BoolP("by-seq", "s", false, "replace seq")</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> replaceCmd.Flags().BoolP("ignore-case", "i", false, "ignore case")</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/seqkit/cmd/root.go</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/seqkit/cmd/root.go</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="p">@@ -62,7 +62,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> RootCmd.PersistentFlags().StringP("seq-type", "t", "auto", "sequence type (dna|rna|protein|unlimit|auto) (for auto, it automatically detect by the first sequence)")</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> RootCmd.PersistentFlags().IntP("threads", "j", defaultThreads, "number of CPUs. (default value: 1 for single-CPU PC, 2 for others)")</span>
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- RootCmd.PersistentFlags().IntP("line-width", "w", 60, "line width when outputing FASTA format (0 for no wrap)")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RootCmd.PersistentFlags().IntP("line-width", "w", 60, "line width when outputting FASTA format (0 for no wrap)")</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> RootCmd.PersistentFlags().StringP("id-regexp", "", fastx.DefaultIDRegexp, "regular expression for parsing ID")</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> RootCmd.PersistentFlags().BoolP("id-ncbi", "", false, "FASTA head is NCBI-style, e.g. >gi|110645304|ref|NC_002516.2| Pseud...")</span>
</pre>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> RootCmd.PersistentFlags().StringP("out-file", "o", "-", `out file ("-" for stdout, suffix .gz for gzipped out)`)</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/seqkit/cmd/shuffle.go</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/seqkit/cmd/shuffle.go</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="p">@@ -46,7 +46,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> supported.</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> Firstly, seqkit reads the sequence IDs. If the file is not plain FASTA file,</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-seqkit will write the sequences to tempory files, and create FASTA index.</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+seqkit will write the sequences to temporary files, and create FASTA index.</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> Secondly, seqkit shuffles sequence IDs and extract sequences by FASTA index.</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="p">@@ -149,7 +149,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> newFile = file + ".fastx"</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> if !quiet {</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- log.Infof("read and write sequences to tempory file: %s ...", newFile)</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ log.Infof("read and write sequences to temporary file: %s ...", newFile)</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> var nseqs int</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="p">@@ -231,5 +231,5 @@</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> RootCmd.AddCommand(shuffleCmd)</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> shuffleCmd.Flags().Int64P("rand-seed", "s", 23, "rand seed for shuffle")</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> shuffleCmd.Flags().BoolP("two-pass", "2", false, "two-pass mode read files twice to lower memory usage. (only for FASTA format)")</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- shuffleCmd.Flags().BoolP("keep-temp", "k", false, "keep tempory FASTA and .fai file when using 2-pass mode")</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ shuffleCmd.Flags().BoolP("keep-temp", "k", false, "keep temporary FASTA and .fai file when using 2-pass mode")</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/seqkit/cmd/sort.go</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/seqkit/cmd/sort.go</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="p">@@ -50,7 +50,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> Firstly, seqkit reads the sequence head and length information.</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> If the file is not plain FASTA file,</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-seqkit will write the sequences to tempory files, and create FASTA index.</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+seqkit will write the sequences to temporary files, and create FASTA index.</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> Secondly, seqkit sorts sequence by head and length information</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> and extracts sequences by FASTA index.</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="p">@@ -240,7 +240,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> newFile = file + ".fastx"</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> if !quiet {</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- log.Infof("read and write sequences to tempory file: %s ...", newFile)</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ log.Infof("read and write sequences to temporary file: %s ...", newFile)</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> var nseqs int</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="p">@@ -440,6 +440,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> sortCmd.Flags().BoolP("ignore-case", "i", false, "ignore case")</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> sortCmd.Flags().BoolP("two-pass", "2", false, "two-pass mode read files twice to lower memory usage. (only for FASTA format)")</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sortCmd.Flags().BoolP("keep-temp", "k", false, "keep tempory FASTA and .fai file when using 2-pass mode")</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sortCmd.Flags().BoolP("keep-temp", "k", false, "keep temporary FASTA and .fai file when using 2-pass mode")</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> sortCmd.Flags().IntP("seq-prefix-length", "L", 10000, "length of sequence prefix on which seqkit sorts by sequences (0 for whole sequence)")</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> }</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/seqkit/cmd/split.go</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/seqkit/cmd/split.go</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="p">@@ -195,7 +195,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> newFile = file + ".fastx"</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> if !quiet {</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- log.Infof("read and write sequences to tempory file: %s ...", newFile)</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ log.Infof("read and write sequences to temporary file: %s ...", newFile)</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> }</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> </span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> var nseqs int</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="p">@@ -361,7 +361,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> newFile = file + ".fastx"</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> }</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> if !quiet {</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- log.Infof("read and write sequences to tempory file: %s ...", newFile)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ log.Infof("read and write sequences to temporary file: %s ...", newFile)</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> }</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> var nseqs int</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="p">@@ -530,7 +530,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> newFile = file + ".fastx"</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> if !quiet {</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- log.Infof("read and write sequences to tempory file: %s ...", newFile)</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ log.Infof("read and write sequences to temporary file: %s ...", newFile)</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> var nseqs int</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="p">@@ -721,7 +721,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> newFile = file + ".fastx"</span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> if !quiet {</span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- log.Infof("read and write sequences to tempory file: %s ...", newFile)</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ log.Infof("read and write sequences to temporary file: %s ...", newFile)</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> var nseqs int</span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="p">@@ -853,7 +853,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> `e.g 1:12 for first 12 bases, -12:-1 for last 12 bases. type "seqkit split -h" for more examples`)</span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> splitCmd.Flags().BoolP("two-pass", "2", false, "two-pass mode read files twice to lower memory usage. (only for FASTA format)")</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> splitCmd.Flags().BoolP("dry-run", "d", false, "dry run, just print message and no files will be created.")</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- splitCmd.Flags().BoolP("keep-temp", "k", false, "keep tempory FASTA and .fai file when using 2-pass mode")</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ splitCmd.Flags().BoolP("keep-temp", "k", false, "keep temporary FASTA and .fai file when using 2-pass mode")</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> splitCmd.Flags().StringP("out-dir", "O", "", "output directory (default value is $infile.split)")</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> splitCmd.Flags().BoolP("force", "f", false, "overwrite output directory")</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#589b0da1474d6fcebfbeb88b464ffa5e9d91a132"><strong>debian/seqkit-benchmark.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SEQKIT-BENCHMARK "1" "August 2020" "seqkit-benchmark 0.12.1+ds" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">seqkit-benchmark \- cross-platform and ultrafast toolkit for FASTA/Q file manipulation</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">feed me one uncompressed FASTA file</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.SH USAGE</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">seqkit-benchmark <fasta-file></span></pre>
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<li id="936f94415260b98c932db319f298c89c1cd7a783">
<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#936f94415260b98c932db319f298c89c1cd7a783"><strong>debian/seqkit.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SEQKIT "1" "August 2020" "seqkit 0.12.1+ds" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">seqkit \- cross-platform and ultrafast toolkit for FASTA/Q file manipulation</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">SeqKit \fB\-\-\fR a cross\-platform and ultrafast toolkit for FASTA/Q file manipulation</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Version: 0.12.1</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Author: Wei Shen <shenwei356@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Documents : http://bioinf.shenwei.me/seqkit</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Source code: https://github.com/shenwei356/seqkit</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Please cite: https://doi.org/10.1371/journal.pone.0163962</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.SS "Usage:"</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">seqkit [command]</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.SS "Available Commands:"</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">amplicon</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">retrieve amplicon (or specific region around it) via primer(s)</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">bam</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">monitoring and online histograms of BAM record features</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">common</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">find common sequences of multiple files by id/name/sequence</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">concat</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">concatenate sequences with same ID from multiple files</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">convert</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">convert FASTQ quality encoding between Sanger, Solexa and Illumina</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.TP</span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">duplicate</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">duplicate sequences N times</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.TP</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">faidx</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">create FASTA index file and extract subsequence</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.TP</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">fish</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">look for short sequences in larger sequences using local alignment</span>
</pre>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.TP</span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">fq2fa</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">convert FASTQ to FASTA</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.TP</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">fx2tab</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">convert FASTA/Q to tabular format (with length/GC content/GC skew)</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.IP</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">genautocomplete generate shell autocompletion script</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">grep search sequences by ID/name/sequence/sequence motifs, mismatch allowed</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">head print first N FASTA/Q records</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">help Help about any command</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">locate locate subsequences/motifs, mismatch allowed</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">mutate edit sequence (point mutation, insertion, deletion)</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">range print FASTA/Q records in a range (start:end)</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">rename rename duplicated IDs</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">replace replace name/sequence by regular expression</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">restart reset start position for circular genome</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">rmdup remove duplicated sequences by id/name/sequence</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">sample sample sequences by number or proportion</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">sana sanitize broken single line fastq files</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">seq transform sequences (revserse, complement, extract ID...)</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">shuffle shuffle sequences</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">sliding sliding sequences, circular genome supported</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">sort sort sequences by id/name/sequence/length</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">split split sequences into files by id/seq region/size/parts (mainly for FASTA)</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">split2 split sequences into files by size/parts (FASTA, PE/SE FASTQ)</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">stats simple statistics of FASTA/Q files</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">subseq get subsequences by region/gtf/bed, including flanking sequences</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">tab2fx convert tabular format to FASTA/Q format</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">translate translate DNA/RNA to protein sequence (supporting ambiguous bases)</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">version print version information and check for update</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">watch monitoring and online histograms of sequence features</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">.SS "Flags:"</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">.TP</span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">\fB\-\-alphabet\-guess\-seq\-length\fR int</span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">length of sequence prefix of the first FASTA record based on which seqkit guesses the sequence type (0 for whole seq) (default 10000)</span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">.TP</span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">help for seqkit</span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">.TP</span>
</pre>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">\fB\-\-id\-ncbi\fR</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">FASTA head is NCBI\-style, e.g. >gi|110645304|ref|NC_002516.2| Pseud...</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">.TP</span>
</pre>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">\fB\-\-id\-regexp\fR string</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">regular expression for parsing ID (default "^(\e\eS+)\e\es?")</span>
</pre>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">.TP</span>
</pre>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">\fB\-\-infile\-list\fR string</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">file of input files list (one file per line), if given, they are appended to files from cli arguments</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">.TP</span>
</pre>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">\fB\-w\fR, \fB\-\-line\-width\fR int</span>
</pre>
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<td class="diff-line-num new new_line" 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="plaintext">line width when outputting FASTA format (0 for no wrap) (default 60)</span>
</pre>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">\fB\-o\fR, \fB\-\-out\-file\fR string</span>
</pre>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">out file ("\-" for stdout, suffix .gz for gzipped out) (default "\-")</span>
</pre>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" 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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">\fB\-\-quiet\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">be quiet and do not show extra information</span>
</pre>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">\fB\-t\fR, \fB\-\-seq\-type\fR string</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">sequence type (dna|rna|protein|unlimit|auto) (for auto, it automatically detect by the first sequence) (default "auto")</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">\fB\-j\fR, \fB\-\-threads\fR int</span>
</pre>
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<td class="diff-line-num new new_line" 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="plaintext">number of CPUs. (default value: 1 for single\-CPU PC, 2 for others) (default 2)</span>
</pre>
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<td class="diff-line-num new new_line" 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="plaintext">.PP</span>
</pre>
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<td class="diff-line-num new new_line" 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="plaintext">Use "seqkit [command] \fB\-\-help\fR" for more information about a command.</span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
</pre>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
</pre>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \</span>
</pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%<span class="idiff left right">,repacksuffix=+ds,dversionmangle=auto</span>" \</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">https://github.com/shenwei356/seqkit/releases .*/archive/v?@ANY_VERSION@\.tar\.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#a14f3e9f63bfcdc0edae53df40500f79a4d10c6b"><strong>tests/pcs109_5k.bam</strong>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#e4e6de67e4bb4c6122d021ab02cae8891dfdfa0d"><strong>tests/pcs109_5k.bam.bai</strong>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#c13ad171ce2c2d2f5b1efc0f554dcd673fd11158"><strong>tests/pcs109_5k_prim.bam</strong>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6#de576c405abafa8a6db072c7f5f292b3e9710034"><strong>tests/pcs109_5k_prim.bam.bai</strong>
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